diff --git a/packages/compiler-sfc/__tests__/compileScript.spec.ts b/packages/compiler-sfc/__tests__/compileScript.spec.ts
index 11b5661c16c..73c6d316a40 100644
--- a/packages/compiler-sfc/__tests__/compileScript.spec.ts
+++ b/packages/compiler-sfc/__tests__/compileScript.spec.ts
@@ -1,5 +1,11 @@
 import { BindingTypes } from '@vue/compiler-core'
-import { assertCode, compileSFCScript as compile, mockId } from './utils'
+import {
+  assertCode,
+  compileSFCScript as compile,
+  getPositionInCode,
+  mockId,
+} from './utils'
+import { type RawSourceMap, SourceMapConsumer } from 'source-map-js'
 
 describe('SFC compile <script setup>', () => {
   test('should compile JS syntax', () => {
@@ -690,6 +696,27 @@ describe('SFC compile <script setup>', () => {
       expect(content).toMatch(`new (_unref(Foo)).Bar()`)
       assertCode(content)
     })
+
+    // #12682
+    test('source map', () => {
+      const source = `
+      <script setup>
+        const count = ref(0)
+      </script>
+      <template>
+        <button @click="throw new Error(\`msg\`);"></button>
+      </template>
+      `
+      const { content, map } = compile(source, { inlineTemplate: true })
+      expect(map).not.toBeUndefined()
+      const consumer = new SourceMapConsumer(map as RawSourceMap)
+      expect(
+        consumer.originalPositionFor(getPositionInCode(content, 'count')),
+      ).toMatchObject(getPositionInCode(source, `count`))
+      expect(
+        consumer.originalPositionFor(getPositionInCode(content, 'Error')),
+      ).toMatchObject(getPositionInCode(source, `Error`))
+    })
   })
 
   describe('with TypeScript', () => {
diff --git a/packages/compiler-sfc/__tests__/compileTemplate.spec.ts b/packages/compiler-sfc/__tests__/compileTemplate.spec.ts
index 2ea1eb9d378..d4ddc763812 100644
--- a/packages/compiler-sfc/__tests__/compileTemplate.spec.ts
+++ b/packages/compiler-sfc/__tests__/compileTemplate.spec.ts
@@ -6,6 +6,7 @@ import {
 } from '../src/compileTemplate'
 import { type SFCTemplateBlock, parse } from '../src/parse'
 import { compileScript } from '../src'
+import { getPositionInCode } from './utils'
 
 function compile(opts: Omit<SFCTemplateCompileOptions, 'id'>) {
   return compileTemplate({
@@ -482,36 +483,3 @@ test('non-identifier expression in legacy filter syntax', () => {
     babelParse(compilationResult.code, { sourceType: 'module' })
   }).not.toThrow()
 })
-
-interface Pos {
-  line: number
-  column: number
-  name?: string
-}
-
-function getPositionInCode(
-  code: string,
-  token: string,
-  expectName: string | boolean = false,
-): Pos {
-  const generatedOffset = code.indexOf(token)
-  let line = 1
-  let lastNewLinePos = -1
-  for (let i = 0; i < generatedOffset; i++) {
-    if (code.charCodeAt(i) === 10 /* newline char code */) {
-      line++
-      lastNewLinePos = i
-    }
-  }
-  const res: Pos = {
-    line,
-    column:
-      lastNewLinePos === -1
-        ? generatedOffset
-        : generatedOffset - lastNewLinePos - 1,
-  }
-  if (expectName) {
-    res.name = typeof expectName === 'string' ? expectName : token
-  }
-  return res
-}
diff --git a/packages/compiler-sfc/__tests__/utils.ts b/packages/compiler-sfc/__tests__/utils.ts
index 5a58a6b58ae..b5cfc9606d5 100644
--- a/packages/compiler-sfc/__tests__/utils.ts
+++ b/packages/compiler-sfc/__tests__/utils.ts
@@ -40,3 +40,36 @@ export function assertCode(code: string): void {
   }
   expect(code).toMatchSnapshot()
 }
+
+interface Pos {
+  line: number
+  column: number
+  name?: string
+}
+
+export function getPositionInCode(
+  code: string,
+  token: string,
+  expectName: string | boolean = false,
+): Pos {
+  const generatedOffset = code.indexOf(token)
+  let line = 1
+  let lastNewLinePos = -1
+  for (let i = 0; i < generatedOffset; i++) {
+    if (code.charCodeAt(i) === 10 /* newline char code */) {
+      line++
+      lastNewLinePos = i
+    }
+  }
+  const res: Pos = {
+    line,
+    column:
+      lastNewLinePos === -1
+        ? generatedOffset
+        : generatedOffset - lastNewLinePos - 1,
+  }
+  if (expectName) {
+    res.name = typeof expectName === 'string' ? expectName : token
+  }
+  return res
+}
diff --git a/packages/compiler-sfc/src/compileScript.ts b/packages/compiler-sfc/src/compileScript.ts
index 8098b43ce45..67af92df5e7 100644
--- a/packages/compiler-sfc/src/compileScript.ts
+++ b/packages/compiler-sfc/src/compileScript.ts
@@ -23,7 +23,11 @@ import type {
   Statement,
 } from '@babel/types'
 import { walk } from 'estree-walker'
-import type { RawSourceMap } from 'source-map-js'
+import {
+  type RawSourceMap,
+  SourceMapConsumer,
+  SourceMapGenerator,
+} from 'source-map-js'
 import {
   normalScriptDefaultVar,
   processNormalScript,
@@ -32,7 +36,6 @@ import { CSS_VARS_HELPER, genCssVarsCode } from './style/cssVars'
 import {
   type SFCTemplateCompileOptions,
   compileTemplate,
-  mergeSourceMaps,
 } from './compileTemplate'
 import { warnOnce } from './warn'
 import { transformDestructuredProps } from './script/definePropsDestructure'
@@ -1034,10 +1037,12 @@ export function compileScript(
           includeContent: true,
         }) as unknown as RawSourceMap)
       : undefined
-  if (map && templateMap) {
+  // merge source maps of the script setup and template in inline mode
+  if (templateMap && map) {
     const offset = content.indexOf(returned)
-    const lineOffset = content.slice(0, offset).split(/\r?\n/).length - 1
-    map = mergeSourceMaps(map, templateMap, lineOffset)
+    const templateLineOffset =
+      content.slice(0, offset).split(/\r?\n/).length - 1
+    map = mergeSourceMaps(map, templateMap, templateLineOffset)
   }
   return {
     ...scriptSetup,
@@ -1301,3 +1306,42 @@ function isStaticNode(node: Node): boolean {
   }
   return false
 }
+
+export function mergeSourceMaps(
+  scriptMap: RawSourceMap,
+  templateMap: RawSourceMap,
+  templateLineOffset: number,
+): RawSourceMap {
+  const generator = new SourceMapGenerator()
+  const addMapping = (map: RawSourceMap, lineOffset = 0) => {
+    const consumer = new SourceMapConsumer(map)
+    ;(consumer as any).sources.forEach((sourceFile: string) => {
+      ;(generator as any)._sources.add(sourceFile)
+      const sourceContent = consumer.sourceContentFor(sourceFile)
+      if (sourceContent != null) {
+        generator.setSourceContent(sourceFile, sourceContent)
+      }
+    })
+    consumer.eachMapping(m => {
+      if (m.originalLine == null) return
+      generator.addMapping({
+        generated: {
+          line: m.generatedLine + lineOffset,
+          column: m.generatedColumn,
+        },
+        original: {
+          line: m.originalLine,
+          column: m.originalColumn,
+        },
+        source: m.source,
+        name: m.name,
+      })
+    })
+  }
+
+  addMapping(scriptMap)
+  addMapping(templateMap, templateLineOffset)
+  ;(generator as any)._sourceRoot = scriptMap.sourceRoot
+  ;(generator as any)._file = scriptMap.file
+  return (generator as any).toJSON()
+}
diff --git a/packages/compiler-sfc/src/compileTemplate.ts b/packages/compiler-sfc/src/compileTemplate.ts
index 7c1d63ea1cb..322b1570e1a 100644
--- a/packages/compiler-sfc/src/compileTemplate.ts
+++ b/packages/compiler-sfc/src/compileTemplate.ts
@@ -327,51 +327,6 @@ function mapLines(oldMap: RawSourceMap, newMap: RawSourceMap): RawSourceMap {
   return generator.toJSON()
 }
 
-export function mergeSourceMaps(
-  scriptMap: RawSourceMap,
-  templateMap: RawSourceMap,
-  templateLineOffset: number,
-): RawSourceMap {
-  if (!templateMap) return scriptMap
-  if (!scriptMap) return templateMap
-
-  const mergedMapGenerator = new SourceMapGenerator() as any
-  const scriptConsumer = new SourceMapConsumer(scriptMap)
-  scriptConsumer.eachMapping(mapping => {
-    if (mapping.originalLine == null) return
-    mergedMapGenerator.addMapping({
-      generated: {
-        line: mapping.generatedLine,
-        column: mapping.generatedColumn,
-      },
-      original: {
-        line: mapping.originalLine,
-        column: mapping.originalColumn,
-      },
-      source: mapping.source,
-      name: mapping.name,
-    })
-  })
-
-  const templateConsumer = new SourceMapConsumer(templateMap)
-  templateConsumer.eachMapping(mapping => {
-    if (mapping.originalLine == null) return
-    mergedMapGenerator.addMapping({
-      generated: {
-        line: mapping.generatedLine + templateLineOffset,
-        column: mapping.generatedColumn,
-      },
-      original: {
-        line: mapping.originalLine,
-        column: mapping.originalColumn,
-      },
-      source: mapping.source,
-      name: mapping.name,
-    })
-  })
-  return mergedMapGenerator.toJSON()
-}
-
 function patchErrors(
   errors: CompilerError[],
   source: string,