diff --git a/src/services/code-graph.ts b/src/services/code-graph.ts
index eb13397..9887bff 100644
--- a/src/services/code-graph.ts
+++ b/src/services/code-graph.ts
@@ -10,7 +10,7 @@ import { EXTRA_EXTENSIONS, getLanguageFromExtension, MAX_GRAPH_FILE_BYTES } from
 import type { CodeGraph, CodeGraphEdge, CodeGraphNode } from "../types.js";
 import { loadPathAliases } from "./graph-aliases.js";
 import { extractImports } from "./graph-imports.js";
-import { resolveImport } from "./graph-resolution.js";
+import { buildJvmSuffixMap, resolveImport } from "./graph-resolution.js";
 import { createIgnoreFilter, shouldIgnore } from "./ignore.js";
 import { logger } from "./logger.js";
 import { deleteGraphData, getGraphMetadata, loadGraphData, saveGraphData } from "./qdrant.js";
@@ -390,6 +390,16 @@ export async function buildCodeGraph(
   const nodesMap = new Map<string, CodeGraphNode>();
   const edges: CodeGraphEdge[] = [];
 
+  // Build a suffix lookup map for JVM multi-module projects (Java/Kotlin/Scala).
+  // This resolves FQNs like com.example.Foo when the class lives under a nested
+  // src/main/java/ tree (e.g. module-a/sub/src/main/java/com/example/Foo.java).
+  // Cost: O(n) once here, O(1) per import lookup — negligible vs. full AST parse.
+  const hasJvm = files.some((f) => {
+    const e = path.extname(f).toLowerCase();
+    return e === ".java" || e === ".kt" || e === ".kts" || e === ".scala";
+  });
+  const jvmSuffixMap = hasJvm ? buildJvmSuffixMap(fileSet) : undefined;
+
   for (const relPath of files) {
     const ext = path.extname(relPath).toLowerCase();
     const lang = getAstGrepLang(ext);
@@ -448,7 +458,7 @@ export async function buildCodeGraph(
       // Try to resolve to a project file
       // CSS imports from <style> blocks use CSS resolution even when the source file is Svelte/Vue
       const resolutionLanguage = imp.isCssImport ? "css" : language;
-      const resolved = resolveImport(imp.moduleSpecifier, absolutePath, resolvedPath, fileSet, resolutionLanguage, aliases);
+      const resolved = resolveImport(imp.moduleSpecifier, absolutePath, resolvedPath, fileSet, resolutionLanguage, aliases, jvmSuffixMap);
       if (resolved) {
         node.dependencies.push(resolved);
 
diff --git a/src/services/graph-resolution.ts b/src/services/graph-resolution.ts
index fe41ffc..fa0269a 100644
--- a/src/services/graph-resolution.ts
+++ b/src/services/graph-resolution.ts
@@ -5,6 +5,52 @@ import type { PathAliases } from "./graph-aliases.js";
 
 // ── Module resolution ────────────────────────────────────────────────────
 
+/**
+ * Build a suffix lookup map for JVM (Java/Kotlin/Scala) files in multi-module projects.
+ *
+ * For a Maven/Gradle multi-module layout such as:
+ *   module-a/sub-module/src/main/java/com/example/Foo.java
+ * the map entry is:
+ *   key:   "com/example/Foo.java"  (platform-normalised with path.sep)
+ *   value: "module-a/sub-module/src/main/java/com/example/Foo.java"
+ *
+ * This enables O(1) resolution of fully-qualified class names that cannot be
+ * found via the standard prefix-based scan (e.g. src/main/java/…).
+ *
+ * Call this once per graph build and pass the result to resolveImport.
+ */
+export function buildJvmSuffixMap(fileSet: Set<string>): Map<string, string> {
+  const map = new Map<string, string>();
+  const jvmExts = new Set([".java", ".kt", ".kts", ".scala"]);
+
+  for (const f of fileSet) {
+    if (!jvmExts.has(path.extname(f))) continue;
+
+    // Split on either separator so the logic works on Windows and POSIX.
+    const parts = f.split(/[\\/]/);
+
+    // Find the first occurrence of src/main/<lang> boundary.
+    const jvmLangs = new Set(["java", "kotlin", "scala"]);
+    const idx = parts.findIndex(
+      (p, i) =>
+        p === "src" &&
+        parts[i + 1] === "main" &&
+        jvmLangs.has(parts[i + 2]),
+    );
+
+    if (idx !== -1) {
+      // classPath = everything after src/main/<lang>, e.g. com/example/Foo.java
+      const classPath = parts.slice(idx + 3).join(path.sep);
+      // Only register the first match to avoid ambiguity for duplicate class names.
+      if (!map.has(classPath)) {
+        map.set(classPath, f);
+      }
+    }
+  }
+
+  return map;
+}
+
 /**
  * Resolve a module specifier to a relative file path within the project.
  * Returns null if the module is external (e.g., npm package, stdlib).
@@ -16,6 +62,7 @@ export function resolveImport(
   fileSet: Set<string>,
   language: string,
   aliases?: PathAliases,
+  jvmSuffixMap?: Map<string, string>,
 ): string | null {
   // Skip obvious external/stdlib modules
   if (isExternalModule(moduleSpecifier, language)) return null;
@@ -89,11 +136,12 @@ export function resolveImport(
       // com.example.Foo → com/example/Foo.java (or .kt, .scala)
       const filePath = moduleSpecifier.replace(/\./g, "/");
       const exts = language === "java" ? [".java"] : language === "kotlin" ? [".kt", ".kts"] : [".scala"];
-      // Try direct resolution from project root
+
+      // 1. Try direct resolution from project root (single-module layout).
       const direct = resolveRelativePath(filePath, projectPath, projectPath, fileSet, exts);
       if (direct) return direct;
 
-      // Try common source directories (Maven/Gradle convention)
+      // 2. Try common source directories (Maven/Gradle single-module convention).
       const jvmSrcDirs = [
         `src/main/${language}`,  // src/main/java, src/main/kotlin, src/main/scala
         "src/main",
@@ -105,6 +153,18 @@ export function resolveImport(
         );
         if (inSrc) return inSrc;
       }
+
+      // 3. Fallback: suffix-map lookup for multi-module Maven/Gradle projects.
+      //    e.g. module-a/sub/src/main/java/com/example/Foo.java
+      //    The map is built once per graph build (O(n)) and looked up in O(1).
+      if (jvmSuffixMap) {
+        for (const ext of exts) {
+          const classPath = filePath.replace(/\//g, path.sep) + ext;
+          const found = jvmSuffixMap.get(classPath);
+          if (found) return found;
+        }
+      }
+
       return null;
     }
 
diff --git a/tests/unit/graph-resolution.test.ts b/tests/unit/graph-resolution.test.ts
index 8977d11..662883e 100644
--- a/tests/unit/graph-resolution.test.ts
+++ b/tests/unit/graph-resolution.test.ts
@@ -5,7 +5,7 @@ import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
 import { afterEach, describe, expect, it } from "vitest";
-import { resolveImport } from "../../src/services/graph-resolution.js";
+import { buildJvmSuffixMap, resolveImport } from "../../src/services/graph-resolution.js";
 
 // ── Helper to create temp project layouts ─────────────────────────────
 
@@ -1206,4 +1206,128 @@ describe("graph-resolution", () => {
       expect(result).toBeNull();
     });
   });
+
+  // ── buildJvmSuffixMap + multi-module resolution ──────────────────────────
+
+  describe("JVM multi-module resolution (buildJvmSuffixMap)", () => {
+    it("builds a suffix map keyed by class path after src/main/java", () => {
+      project = createTempProject({
+        [`module-a${path.sep}sub${path.sep}src${path.sep}main${path.sep}java${path.sep}com${path.sep}example${path.sep}Foo.java`]: "",
+        [`module-b${path.sep}src${path.sep}main${path.sep}kotlin${path.sep}com${path.sep}example${path.sep}Bar.kt`]: "",
+        [`module-c${path.sep}src${path.sep}main${path.sep}scala${path.sep}com${path.sep}example${path.sep}Baz.scala`]: "",
+      });
+
+      const map = buildJvmSuffixMap(project.fileSet);
+
+      expect(map.has(`com${path.sep}example${path.sep}Foo.java`)).toBe(true);
+      expect(map.has(`com${path.sep}example${path.sep}Bar.kt`)).toBe(true);
+      expect(map.has(`com${path.sep}example${path.sep}Baz.scala`)).toBe(true);
+    });
+
+    it("returns empty map when project has no JVM files", () => {
+      project = createTempProject({ "index.ts": "", "style.css": "" });
+      const map = buildJvmSuffixMap(project.fileSet);
+      expect(map.size).toBe(0);
+    });
+
+    it("ignores JVM files outside src/main/<lang> (e.g. test sources)", () => {
+      project = createTempProject({
+        // test source — should be ignored
+        [`module-a${path.sep}src${path.sep}test${path.sep}java${path.sep}com${path.sep}example${path.sep}FooTest.java`]: "",
+        // main source — should be registered
+        [`module-a${path.sep}src${path.sep}main${path.sep}java${path.sep}com${path.sep}example${path.sep}Foo.java`]: "",
+      });
+
+      const map = buildJvmSuffixMap(project.fileSet);
+      expect(map.has(`com${path.sep}example${path.sep}Foo.java`)).toBe(true);
+      expect(map.has(`com${path.sep}example${path.sep}FooTest.java`)).toBe(false);
+    });
+
+    it("resolves a Java import in a multi-module Maven project via suffix map", () => {
+      // Simulate: module-sso/module-sso-service/src/main/java/cn/sino/sso/UserService.java
+      const userServicePath =
+        `module-sso${path.sep}module-sso-service${path.sep}src${path.sep}main${path.sep}java${path.sep}cn${path.sep}sino${path.sep}sso${path.sep}UserService.java`;
+      const callerPath =
+        `module-opt${path.sep}src${path.sep}main${path.sep}java${path.sep}cn${path.sep}sino${path.sep}opt${path.sep}Service.java`;
+
+      project = createTempProject({
+        [userServicePath]: "",
+        [callerPath]: "",
+      });
+
+      const jvmSuffixMap = buildJvmSuffixMap(project.fileSet);
+
+      const result = resolveImport(
+        "cn.sino.sso.UserService",
+        path.join(project.root, callerPath),
+        project.root,
+        project.fileSet,
+        "java",
+        undefined,
+        jvmSuffixMap,
+      );
+
+      expect(result).toBe(userServicePath);
+    });
+
+    it("resolves Kotlin import in multi-module project via suffix map", () => {
+      const barPath =
+        `module-core${path.sep}src${path.sep}main${path.sep}kotlin${path.sep}com${path.sep}example${path.sep}Bar.kt`;
+      const callerPath =
+        `module-api${path.sep}src${path.sep}main${path.sep}kotlin${path.sep}com${path.sep}example${path.sep}Caller.kt`;
+
+      project = createTempProject({ [barPath]: "", [callerPath]: "" });
+
+      const jvmSuffixMap = buildJvmSuffixMap(project.fileSet);
+      const result = resolveImport(
+        "com.example.Bar",
+        path.join(project.root, callerPath),
+        project.root,
+        project.fileSet,
+        "kotlin",
+        undefined,
+        jvmSuffixMap,
+      );
+
+      expect(result).toBe(barPath);
+    });
+
+    it("returns null when class exists nowhere in the project", () => {
+      project = createTempProject({
+        [`module-a${path.sep}src${path.sep}main${path.sep}java${path.sep}com${path.sep}example${path.sep}Foo.java`]: "",
+      });
+
+      const jvmSuffixMap = buildJvmSuffixMap(project.fileSet);
+      const result = resolveImport(
+        "com.example.NonExistent",
+        path.join(project.root, `module-a${path.sep}src${path.sep}main${path.sep}java${path.sep}com${path.sep}example${path.sep}Foo.java`),
+        project.root,
+        project.fileSet,
+        "java",
+        undefined,
+        jvmSuffixMap,
+      );
+
+      expect(result).toBeNull();
+    });
+
+    it("still returns null for java stdlib even with suffix map", () => {
+      project = createTempProject({
+        [`module-a${path.sep}src${path.sep}main${path.sep}java${path.sep}java${path.sep}util${path.sep}List.java`]: "",
+      });
+
+      const jvmSuffixMap = buildJvmSuffixMap(project.fileSet);
+      const result = resolveImport(
+        "java.util.List",
+        path.join(project.root, `module-a${path.sep}src${path.sep}main${path.sep}java${path.sep}Caller.java`),
+        project.root,
+        project.fileSet,
+        "java",
+        undefined,
+        jvmSuffixMap,
+      );
+
+      expect(result).toBeNull();
+    });
+  });
 });