diff --git a/apps/cli/src/import/stream-import.test.ts b/apps/cli/src/import/stream-import.test.ts
index e5beb8a5..8dc856b0 100644
--- a/apps/cli/src/import/stream-import.test.ts
+++ b/apps/cli/src/import/stream-import.test.ts
@@ -4,8 +4,13 @@ import os from 'node:os'
 import path from 'node:path'
 import test from 'node:test'
 import type { PathProvider } from '@openchatlab/core'
-import { DatabaseManager, readDataDirCompatibilityMeta } from '@openchatlab/node-runtime'
-import { incrementalImport } from './stream-import'
+import {
+  DatabaseManager,
+  DataDirCompatibilityError,
+  raiseDataDirMinRuntimeVersion,
+  readDataDirCompatibilityMeta,
+} from '@openchatlab/node-runtime'
+import { analyzeIncrementalImport, incrementalImport } from './stream-import'
 
 const nativeBinding = path.resolve('apps/cli/native/better_sqlite3.node')
 
@@ -79,3 +84,29 @@ test('incrementalImport raises the data directory gate after successful writes',
   assert.equal(meta?.dataCompatibilityVersion, 1)
   assert.deepEqual(meta?.reasons, ['segment-schema'])
 })
+
+test('analyzeIncrementalImport propagates data directory compatibility errors', async () => {
+  const root = makeTempDir()
+  const pathProvider = createPathProvider(root)
+  fs.mkdirSync(pathProvider.getDatabaseDir(), { recursive: true })
+  fs.writeFileSync(path.join(pathProvider.getDatabaseDir(), 'existing.db'), 'not opened before compatibility check')
+  raiseDataDirMinRuntimeVersion(pathProvider, {
+    minRuntimeVersion: '0.26.0',
+    dataCompatibilityVersion: 2,
+    reason: 'future-schema',
+    runtime: { version: '0.26.0', kind: 'desktop' },
+    module: 'future-migration',
+    now: () => 1780830000,
+  })
+  const manager = new DatabaseManager(pathProvider, {
+    nativeBinding,
+    runtime: { version: '0.25.1', kind: 'cli' },
+  })
+  const filePath = path.join(root, 'incremental.jsonl')
+  writeIncrementalJsonl(filePath)
+
+  await assert.rejects(
+    () => analyzeIncrementalImport(manager, 'existing', filePath),
+    (error) => error instanceof DataDirCompatibilityError && error.code === 'DATA_DIR_REQUIRES_NEWER_RUNTIME'
+  )
+})
diff --git a/apps/cli/src/import/stream-import.ts b/apps/cli/src/import/stream-import.ts
index 3d8ca633..5a572f66 100644
--- a/apps/cli/src/import/stream-import.ts
+++ b/apps/cli/src/import/stream-import.ts
@@ -223,7 +223,16 @@ export async function analyzeIncrementalImport(
   filePath: string,
   onProgress?: ImportProgressCallback
 ): Promise<IncrementalAnalyzeResult> {
-  return sharedAnalyzeIncremental(sessionId, filePath, buildIncrementalDeps(dbManager, onProgress))
+  let compatibilityError: DataDirCompatibilityError | null = null
+  const result = await sharedAnalyzeIncremental(
+    sessionId,
+    filePath,
+    buildIncrementalDeps(dbManager, onProgress, (error) => {
+      compatibilityError = error
+    })
+  )
+  if (compatibilityError) throw compatibilityError
+  return result
 }
 
 export async function analyzeNewImport(
diff --git a/apps/desktop/main/api/errors.test.ts b/apps/desktop/main/api/errors.test.ts
new file mode 100644
index 00000000..3b33e5f9
--- /dev/null
+++ b/apps/desktop/main/api/errors.test.ts
@@ -0,0 +1,23 @@
+import assert from 'node:assert/strict'
+import test from 'node:test'
+import { DataDirCompatibilityError } from '@openchatlab/node-runtime/src/data-dir-compat'
+import { ApiErrorCode, apiErrorFromUnknown } from './errors'
+
+test('apiErrorFromUnknown maps wrapped data directory compatibility errors to 409', () => {
+  const cause = new DataDirCompatibilityError(
+    'DATA_DIR_REQUIRES_NEWER_RUNTIME',
+    'ChatLab data directory requires runtime version 0.25.1 or newer; current version is 0.25.0.',
+    {
+      userDataDir: '/tmp/chatlab-data',
+      metaPath: '/tmp/chatlab-data/.chatlab-meta.json',
+      currentVersion: '0.25.0',
+      minRuntimeVersion: '0.25.1',
+    }
+  )
+
+  const apiError = apiErrorFromUnknown(new Error('Desktop startup formatted message', { cause }))
+
+  assert.equal(apiError?.code, ApiErrorCode.DATA_DIR_INCOMPATIBLE)
+  assert.equal(apiError?.statusCode, 409)
+  assert.match(apiError?.message ?? '', /requires runtime version 0\.25\.1/)
+})
diff --git a/apps/desktop/main/api/errors.ts b/apps/desktop/main/api/errors.ts
index 00060835..34f6b530 100644
--- a/apps/desktop/main/api/errors.ts
+++ b/apps/desktop/main/api/errors.ts
@@ -2,6 +2,8 @@
  * ChatLab API — Error codes and factory functions
  */
 
+import { DataDirCompatibilityError } from '@openchatlab/node-runtime/src/data-dir-compat'
+
 export enum ApiErrorCode {
   UNAUTHORIZED = 'UNAUTHORIZED',
   SESSION_NOT_FOUND = 'SESSION_NOT_FOUND',
@@ -15,6 +17,7 @@ export enum ApiErrorCode {
   IDEMPOTENCY_CONFLICT = 'IDEMPOTENCY_CONFLICT',
   IDEMPOTENCY_PENDING = 'IDEMPOTENCY_PENDING',
   IMPORT_FAILED = 'IMPORT_FAILED',
+  DATA_DIR_INCOMPATIBLE = 'DATA_DIR_INCOMPATIBLE',
   SERVER_ERROR = 'SERVER_ERROR',
 }
 
@@ -31,6 +34,7 @@ const HTTP_STATUS: Record<ApiErrorCode, number> = {
   [ApiErrorCode.IDEMPOTENCY_CONFLICT]: 409,
   [ApiErrorCode.IDEMPOTENCY_PENDING]: 409,
   [ApiErrorCode.IMPORT_FAILED]: 500,
+  [ApiErrorCode.DATA_DIR_INCOMPATIBLE]: 409,
   [ApiErrorCode.SERVER_ERROR]: 500,
 }
 
@@ -89,10 +93,27 @@ export function importFailed(message: string): ApiError {
   return new ApiError(ApiErrorCode.IMPORT_FAILED, message)
 }
 
+export function dataDirIncompatible(message: string): ApiError {
+  return new ApiError(ApiErrorCode.DATA_DIR_INCOMPATIBLE, message)
+}
+
 export function serverError(message = 'Internal server error'): ApiError {
   return new ApiError(ApiErrorCode.SERVER_ERROR, message)
 }
 
+export function apiErrorFromUnknown(error: unknown): ApiError | null {
+  if (error instanceof ApiError) return error
+  const compatibilityError = findDataDirCompatibilityError(error)
+  if (compatibilityError) return dataDirIncompatible(compatibilityError.message)
+  return null
+}
+
+function findDataDirCompatibilityError(error: unknown): DataDirCompatibilityError | null {
+  if (error instanceof DataDirCompatibilityError) return error
+  if (error instanceof Error && error.cause) return findDataDirCompatibilityError(error.cause)
+  return null
+}
+
 export function successResponse<T>(data: T, meta?: Record<string, unknown>) {
   return {
     success: true as const,
diff --git a/apps/desktop/main/api/routes/import.ts b/apps/desktop/main/api/routes/import.ts
index 7b4057a8..58bf2f4e 100644
--- a/apps/desktop/main/api/routes/import.ts
+++ b/apps/desktop/main/api/routes/import.ts
@@ -24,6 +24,7 @@ import {
   ApiError,
   ApiErrorCode,
   successResponse,
+  apiErrorFromUnknown,
   importInProgress,
   importFailed,
   invalidFormat,
@@ -328,6 +329,11 @@ async function handleUnifiedImport(request: FastifyRequest, reply: FastifyReply,
   } catch (error: any) {
     idempotencyFail(cacheKey)
     apiLogger.error('Import error', error)
+    const apiError = apiErrorFromUnknown(error)
+    if (apiError) {
+      reply.code(apiError.statusCode).send(errorResponse(apiError))
+      return
+    }
     const err = importFailed(error.message || 'Import process error')
     reply.code(err.statusCode).send(errorResponse(err))
   } finally {
@@ -421,6 +427,11 @@ async function handleLegacyImport(request: FastifyRequest, reply: FastifyReply,
     }
   } catch (error: any) {
     apiLogger.error('Import error', error)
+    const apiError = apiErrorFromUnknown(error)
+    if (apiError) {
+      reply.code(apiError.statusCode).send(errorResponse(apiError))
+      return
+    }
     const err = importFailed(error.message || 'Import process error')
     reply.code(err.statusCode).send(errorResponse(err))
   } finally {
diff --git a/apps/desktop/main/api/server.ts b/apps/desktop/main/api/server.ts
index 482f2534..8670170d 100644
--- a/apps/desktop/main/api/server.ts
+++ b/apps/desktop/main/api/server.ts
@@ -4,7 +4,7 @@
 
 import Fastify, { type FastifyInstance, type FastifyError } from 'fastify'
 import { authHook } from './auth'
-import { ApiError, ApiErrorCode, errorResponse, serverError } from './errors'
+import { ApiError, ApiErrorCode, apiErrorFromUnknown, errorResponse, serverError } from './errors'
 import { apiLogger } from './logger'
 
 const JSON_BODY_LIMIT = 50 * 1024 * 1024 // 50MB
@@ -23,6 +23,12 @@ export function createServer(): FastifyInstance {
       return
     }
 
+    const apiError = apiErrorFromUnknown(error)
+    if (apiError) {
+      reply.code(apiError.statusCode).send(errorResponse(apiError))
+      return
+    }
+
     if (error.statusCode === 413) {
       const bodyErr = new ApiError(ApiErrorCode.BODY_TOO_LARGE, 'Request body exceeds 50MB limit')
       reply.code(413).send(errorResponse(bodyErr))
diff --git a/packages/mcp-server/src/bin.test.ts b/packages/mcp-server/src/bin.test.ts
new file mode 100644
index 00000000..252e9df1
--- /dev/null
+++ b/packages/mcp-server/src/bin.test.ts
@@ -0,0 +1,30 @@
+import assert from 'node:assert/strict'
+import fs from 'node:fs'
+import os from 'node:os'
+import path from 'node:path'
+import test from 'node:test'
+import { DataDirCompatibilityError, raiseDataDirMinRuntimeVersion } from '@openchatlab/node-runtime'
+import { initStandaloneMcpRuntime } from './standalone-runtime'
+
+function makeTempDir(): string {
+  const baseDir = fs.existsSync('/private/tmp') ? '/private/tmp' : os.tmpdir()
+  return fs.mkdtempSync(path.join(baseDir, 'chatlab-mcp-bin-'))
+}
+
+test('initStandaloneMcpRuntime rejects incompatible data directories before stdio startup', () => {
+  const userDataDir = makeTempDir()
+  const pathProvider = initStandaloneMcpRuntime('0.26.0', userDataDir).pathProvider
+  raiseDataDirMinRuntimeVersion(pathProvider, {
+    minRuntimeVersion: '0.26.0',
+    dataCompatibilityVersion: 2,
+    reason: 'future-schema',
+    runtime: { version: '0.26.0', kind: 'desktop' },
+    module: 'future-migration',
+    now: () => 1780830000,
+  })
+
+  assert.throws(
+    () => initStandaloneMcpRuntime('0.25.1', userDataDir),
+    (error) => error instanceof DataDirCompatibilityError && error.code === 'DATA_DIR_REQUIRES_NEWER_RUNTIME'
+  )
+})
diff --git a/packages/mcp-server/src/bin.ts b/packages/mcp-server/src/bin.ts
index 9e820f9c..9d83e0bf 100644
--- a/packages/mcp-server/src/bin.ts
+++ b/packages/mcp-server/src/bin.ts
@@ -8,17 +8,15 @@
  */
 
 import { loadConfig } from '@openchatlab/config'
-import { NodePathProvider, DatabaseManager } from '@openchatlab/node-runtime'
 import { startMcpServer } from './server'
+import { initStandaloneMcpRuntime } from './standalone-runtime'
 import { getMcpPackageVersion } from './runtime-version'
 
 function main(): void {
   const config = loadConfig()
   const userDataDir = config.data.user_data_dir || undefined
-  const pathProvider = new NodePathProvider(userDataDir)
-  pathProvider.ensureAllDirs()
   const version = getMcpPackageVersion()
-  const dbManager = new DatabaseManager(pathProvider, { runtime: { version, kind: 'mcp' } })
+  const { dbManager } = initStandaloneMcpRuntime(version, userDataDir)
 
   startMcpServer({ version, dbManager }).catch((err) => {
     console.error('[chatlab-mcp] Fatal error:', err)
diff --git a/packages/mcp-server/src/standalone-runtime.ts b/packages/mcp-server/src/standalone-runtime.ts
new file mode 100644
index 00000000..7324c545
--- /dev/null
+++ b/packages/mcp-server/src/standalone-runtime.ts
@@ -0,0 +1,18 @@
+import {
+  assertDataDirCompatible,
+  DatabaseManager,
+  NodePathProvider,
+  type RuntimeIdentity,
+} from '@openchatlab/node-runtime'
+
+export function initStandaloneMcpRuntime(
+  version: string,
+  userDataDir?: string
+): { dbManager: DatabaseManager; pathProvider: NodePathProvider; runtime: RuntimeIdentity } {
+  const pathProvider = new NodePathProvider(userDataDir)
+  pathProvider.ensureAllDirs()
+  const runtime: RuntimeIdentity = { version, kind: 'mcp' }
+  assertDataDirCompatible(pathProvider, runtime)
+  const dbManager = new DatabaseManager(pathProvider, { runtime })
+  return { dbManager, pathProvider, runtime }
+}