diff --git a/src-tauri/src/gemini_mcp.rs b/src-tauri/src/gemini_mcp.rs
index c87a16c9c..62a959c18 100644
--- a/src-tauri/src/gemini_mcp.rs
+++ b/src-tauri/src/gemini_mcp.rs
@@ -42,8 +42,8 @@ fn write_json_value(path: &Path, value: &Value) -> Result<(), AppError> {
 ///
 /// 执行反向格式转换以保持与统一 MCP 结构的兼容性：
 /// - httpUrl → url + type: "http"
-/// - 仅有 url 字段 → 保持不变（SSE 类型）
-/// - 仅有 command 字段 → 保持不变（stdio 类型）
+/// - 仅有 url 字段 → 补齐 type: "sse"（Gemini 以字段名推断传输类型）
+/// - 仅有 command 字段 → 补齐 type: "stdio"
 pub fn read_mcp_servers_map() -> Result<std::collections::HashMap<String, Value>, AppError> {
     let path = user_config_path();
     if !path.exists() {
@@ -65,8 +65,15 @@ pub fn read_mcp_servers_map() -> Result<std::collections::HashMap<String, Value>
                 obj.insert("url".to_string(), http_url);
                 obj.insert("type".to_string(), Value::String("http".to_string()));
             }
-            // 如果有 url 但没有 type，不添加 type（默认为 SSE）
-            // 如果有 command 但没有 type，不添加 type（默认为 stdio）
+
+            // Gemini CLI 不使用 type 字段：这里补齐成统一结构，便于校验与导入
+            if obj.get("type").is_none() {
+                if obj.contains_key("command") {
+                    obj.insert("type".to_string(), Value::String("stdio".to_string()));
+                } else if obj.contains_key("url") {
+                    obj.insert("type".to_string(), Value::String("sse".to_string()));
+                }
+            }
         }
     }
 
diff --git a/src-tauri/src/mcp/codex.rs b/src-tauri/src/mcp/codex.rs
index a82ff75bf..437614128 100644
--- a/src-tauri/src/mcp/codex.rs
+++ b/src-tauri/src/mcp/codex.rs
@@ -376,7 +376,8 @@ pub fn sync_single_server_to_codex(
     doc["mcp_servers"][id] = Item::Table(toml_table);
 
     // 写回文件
-    std::fs::write(&config_path, doc.to_string()).map_err(|e| AppError::io(&config_path, e))?;
+    let new_text = doc.to_string();
+    crate::config::write_text_file(&config_path, &new_text)?;
 
     Ok(())
 }
@@ -412,7 +413,8 @@ pub fn remove_server_from_codex(id: &str) -> Result<(), AppError> {
     }
 
     // 写回文件
-    std::fs::write(&config_path, doc.to_string()).map_err(|e| AppError::io(&config_path, e))?;
+    let new_text = doc.to_string();
+    crate::config::write_text_file(&config_path, &new_text)?;
 
     Ok(())
 }
diff --git a/src-tauri/src/services/mcp.rs b/src-tauri/src/services/mcp.rs
index 4f95c950a..29f821d57 100644
--- a/src-tauri/src/services/mcp.rs
+++ b/src-tauri/src/services/mcp.rs
@@ -17,8 +17,27 @@ impl McpService {
 
     /// 添加或更新 MCP 服务器
     pub fn upsert_server(state: &AppState, server: McpServer) -> Result<(), AppError> {
+        // 读取旧状态：用于处理“编辑时取消勾选某个应用”的场景（需要从对应 live 配置中移除）
+        let prev_apps = state
+            .db
+            .get_all_mcp_servers()?
+            .get(&server.id)
+            .map(|s| s.apps.clone())
+            .unwrap_or_default();
+
         state.db.save_mcp_server(&server)?;
 
+        // 处理禁用：若旧版本启用但新版本取消，则需要从该应用的 live 配置移除
+        if prev_apps.claude && !server.apps.claude {
+            Self::remove_server_from_app(state, &server.id, &AppType::Claude)?;
+        }
+        if prev_apps.codex && !server.apps.codex {
+            Self::remove_server_from_app(state, &server.id, &AppType::Codex)?;
+        }
+        if prev_apps.gemini && !server.apps.gemini {
+            Self::remove_server_from_app(state, &server.id, &AppType::Gemini)?;
+        }
+
         // 同步到各个启用的应用
         Self::sync_server_to_apps(state, &server)?;
 
@@ -190,10 +209,22 @@ impl McpService {
         // 如果有导入的服务器，保存到数据库
         if count > 0 {
             if let Some(servers) = &temp_config.mcp.servers {
+                let mut existing = state.db.get_all_mcp_servers()?;
                 for server in servers.values() {
-                    state.db.save_mcp_server(server)?;
-                    // 同步到 Claude live 配置
-                    Self::sync_server_to_apps(state, server)?;
+                    // 已存在：仅启用 Claude，不覆盖其他字段（与导入模块语义保持一致）
+                    let to_save = if let Some(existing_server) = existing.get(&server.id) {
+                        let mut merged = existing_server.clone();
+                        merged.apps.claude = true;
+                        merged
+                    } else {
+                        server.clone()
+                    };
+
+                    state.db.save_mcp_server(&to_save)?;
+                    existing.insert(to_save.id.clone(), to_save.clone());
+
+                    // 同步到对应应用 live 配置
+                    Self::sync_server_to_apps(state, &to_save)?;
                 }
             }
         }
@@ -212,10 +243,22 @@ impl McpService {
         // 如果有导入的服务器，保存到数据库
         if count > 0 {
             if let Some(servers) = &temp_config.mcp.servers {
+                let mut existing = state.db.get_all_mcp_servers()?;
                 for server in servers.values() {
-                    state.db.save_mcp_server(server)?;
-                    // 同步到 Codex live 配置
-                    Self::sync_server_to_apps(state, server)?;
+                    // 已存在：仅启用 Codex，不覆盖其他字段（与导入模块语义保持一致）
+                    let to_save = if let Some(existing_server) = existing.get(&server.id) {
+                        let mut merged = existing_server.clone();
+                        merged.apps.codex = true;
+                        merged
+                    } else {
+                        server.clone()
+                    };
+
+                    state.db.save_mcp_server(&to_save)?;
+                    existing.insert(to_save.id.clone(), to_save.clone());
+
+                    // 同步到对应应用 live 配置
+                    Self::sync_server_to_apps(state, &to_save)?;
                 }
             }
         }
@@ -234,10 +277,22 @@ impl McpService {
         // 如果有导入的服务器，保存到数据库
         if count > 0 {
             if let Some(servers) = &temp_config.mcp.servers {
+                let mut existing = state.db.get_all_mcp_servers()?;
                 for server in servers.values() {
-                    state.db.save_mcp_server(server)?;
-                    // 同步到 Gemini live 配置
-                    Self::sync_server_to_apps(state, server)?;
+                    // 已存在：仅启用 Gemini，不覆盖其他字段（与导入模块语义保持一致）
+                    let to_save = if let Some(existing_server) = existing.get(&server.id) {
+                        let mut merged = existing_server.clone();
+                        merged.apps.gemini = true;
+                        merged
+                    } else {
+                        server.clone()
+                    };
+
+                    state.db.save_mcp_server(&to_save)?;
+                    existing.insert(to_save.id.clone(), to_save.clone());
+
+                    // 同步到对应应用 live 配置
+                    Self::sync_server_to_apps(state, &to_save)?;
                 }
             }
         }
diff --git a/src-tauri/tests/mcp_commands.rs b/src-tauri/tests/mcp_commands.rs
index 2474d03ed..50508a1a8 100644
--- a/src-tauri/tests/mcp_commands.rs
+++ b/src-tauri/tests/mcp_commands.rs
@@ -246,3 +246,157 @@ fn set_mcp_enabled_for_codex_writes_live_config() {
         "codex config should include the enabled server definition"
     );
 }
+
+#[test]
+fn upsert_mcp_server_disabling_app_removes_from_claude_live_config() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    ensure_test_home();
+
+    // 先创建一个启用 Claude 的 MCP 服务器
+    let state = support::create_test_state().expect("create test state");
+    McpService::upsert_server(
+        &state,
+        McpServer {
+            id: "echo".to_string(),
+            name: "echo".to_string(),
+            server: json!({
+                "type": "stdio",
+                "command": "echo"
+            }),
+            apps: McpApps {
+                claude: true,
+                codex: false,
+                gemini: false,
+            },
+            description: None,
+            homepage: None,
+            docs: None,
+            tags: Vec::new(),
+        },
+    )
+    .expect("upsert should sync to Claude live config");
+
+    // 确认已写入 ~/.claude.json
+    let mcp_path = get_claude_mcp_path();
+    let text = fs::read_to_string(&mcp_path).expect("read ~/.claude.json");
+    let v: serde_json::Value = serde_json::from_str(&text).expect("parse ~/.claude.json");
+    assert!(
+        v.pointer("/mcpServers/echo").is_some(),
+        "echo should exist in Claude live config after enabling"
+    );
+
+    // 再次 upsert：取消勾选 Claude（apps.claude=false），应从 Claude live 配置中移除
+    McpService::upsert_server(
+        &state,
+        McpServer {
+            id: "echo".to_string(),
+            name: "echo".to_string(),
+            server: json!({
+                "type": "stdio",
+                "command": "echo"
+            }),
+            apps: McpApps {
+                claude: false,
+                codex: false,
+                gemini: false,
+            },
+            description: None,
+            homepage: None,
+            docs: None,
+            tags: Vec::new(),
+        },
+    )
+    .expect("upsert disabling app should remove from Claude live config");
+
+    let text = fs::read_to_string(&mcp_path).expect("read ~/.claude.json after disable");
+    let v: serde_json::Value = serde_json::from_str(&text).expect("parse ~/.claude.json");
+    assert!(
+        v.pointer("/mcpServers/echo").is_none(),
+        "echo should be removed from Claude live config after disabling"
+    );
+}
+
+#[test]
+fn import_mcp_from_multiple_apps_merges_enabled_flags() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    let home = ensure_test_home();
+
+    // 1) Claude: ~/.claude.json
+    let mcp_path = get_claude_mcp_path();
+    let claude_json = json!({
+        "mcpServers": {
+            "shared": {
+                "type": "stdio",
+                "command": "echo"
+            }
+        }
+    });
+    fs::write(
+        &mcp_path,
+        serde_json::to_string_pretty(&claude_json).expect("serialize claude mcp"),
+    )
+    .expect("seed ~/.claude.json");
+
+    // 2) Codex: ~/.codex/config.toml
+    let codex_dir = home.join(".codex");
+    fs::create_dir_all(&codex_dir).expect("create codex dir");
+    fs::write(
+        codex_dir.join("config.toml"),
+        r#"[mcp_servers.shared]
+type = "stdio"
+command = "echo"
+"#,
+    )
+    .expect("seed ~/.codex/config.toml");
+
+    let state = support::create_test_state().expect("create test state");
+
+    McpService::import_from_claude(&state).expect("import from claude");
+    McpService::import_from_codex(&state).expect("import from codex");
+
+    let servers = state.db.get_all_mcp_servers().expect("get all mcp servers");
+    let entry = servers.get("shared").expect("shared server exists");
+    assert!(entry.apps.claude, "shared should enable Claude");
+    assert!(entry.apps.codex, "shared should enable Codex");
+}
+
+#[test]
+fn import_mcp_from_gemini_sse_url_only_is_valid() {
+    let _guard = test_mutex().lock().expect("acquire test mutex");
+    reset_test_fs();
+    let home = ensure_test_home();
+
+    // Gemini MCP 位于 ~/.gemini/settings.json
+    let gemini_dir = home.join(".gemini");
+    fs::create_dir_all(&gemini_dir).expect("create gemini dir");
+    let settings_path = gemini_dir.join("settings.json");
+
+    // Gemini SSE：只包含 url（Gemini 不使用 type 字段）
+    let gemini_settings = json!({
+        "mcpServers": {
+            "sse-server": {
+                "url": "https://example.com/sse"
+            }
+        }
+    });
+    fs::write(
+        &settings_path,
+        serde_json::to_string_pretty(&gemini_settings).expect("serialize gemini settings"),
+    )
+    .expect("seed ~/.gemini/settings.json");
+
+    let state = support::create_test_state().expect("create test state");
+    let changed = McpService::import_from_gemini(&state).expect("import from gemini");
+    assert!(changed > 0, "should import at least 1 server");
+
+    let servers = state.db.get_all_mcp_servers().expect("get all mcp servers");
+    let entry = servers.get("sse-server").expect("sse-server exists");
+    assert!(entry.apps.gemini, "imported server should enable Gemini");
+    assert_eq!(
+        entry.server.get("type").and_then(|v| v.as_str()),
+        Some("sse"),
+        "Gemini url-only server should be normalized to type=sse in unified structure"
+    );
+}