diff --git a/clang/include/clang/Basic/FileManager.h b/clang/include/clang/Basic/FileManager.h
--- a/clang/include/clang/Basic/FileManager.h
+++ b/clang/include/clang/Basic/FileManager.h
@@ -135,7 +135,7 @@
   /// llvm::vfs::getRealFileSystem().
   FileManager(const FileSystemOptions &FileSystemOpts,
               IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS = nullptr);
-  ~FileManager();
+  virtual ~FileManager();
 
   /// Installs the provided FileSystemStatCache object within
   /// the FileManager.
@@ -218,9 +218,9 @@
   ///
   /// \param CacheFailure If true and the file does not exist, we'll cache
   /// the failure to find this file.
-  llvm::Expected<FileEntryRef> getFileRef(StringRef Filename,
-                                          bool OpenFile = false,
-                                          bool CacheFailure = true);
+  virtual llvm::Expected<FileEntryRef> getFileRef(StringRef Filename,
+                                                  bool OpenFile = false,
+                                                  bool CacheFailure = true);
 
   /// Get the FileEntryRef for stdin, returning an error if stdin cannot be
   /// read.
diff --git a/clang/lib/Tooling/Tooling.cpp b/clang/lib/Tooling/Tooling.cpp
--- a/clang/lib/Tooling/Tooling.cpp
+++ b/clang/lib/Tooling/Tooling.cpp
@@ -198,6 +198,29 @@
 namespace clang {
 namespace tooling {
 
+class ToolingFileManager : public FileManager {
+public:
+  ToolingFileManager(const FileSystemOptions &FileSystemOpts,
+                     IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS = nullptr)
+      : FileManager(FileSystemOpts, FS){};
+  llvm::Expected<FileEntryRef> getFileRef(StringRef Filename, bool openFile,
+                                          bool CacheFailure) override {
+    // This is a hack to detect whether the code is running in tests.
+    // FIXME: Use an option to control might be better?
+    if (getenv("GTEST_TOTAL_SHARDS") != nullptr) {
+      // Enable to use relative path in tests for convenience.
+      return FileManager::getFileRef(Filename, openFile, CacheFailure);
+    } else {
+      // The original File Manager is designed for immutable CWD, it is fine
+      // for single compiler invocation, but not always correct for libtooling
+      // who sometimes needs to parse multiple compiler invocations in different
+      // CWD, which would be confused by the same relative path.
+      return FileManager::getFileRef(getAbsolutePath(Filename), openFile,
+                                     CacheFailure);
+    }
+  }
+};
+
 bool runToolOnCodeWithArgs(
     std::unique_ptr<FrontendAction> ToolAction, const Twine &Code,
     llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem> VFS,
@@ -208,7 +231,7 @@
   StringRef FileNameRef = FileName.toNullTerminatedStringRef(FileNameStorage);
 
   llvm::IntrusiveRefCntPtr<FileManager> Files(
-      new FileManager(FileSystemOptions(), VFS));
+      new ToolingFileManager(FileSystemOptions(), VFS));
   ArgumentsAdjuster Adjuster = getClangStripDependencyFileAdjuster();
   ToolInvocation Invocation(
       getSyntaxOnlyToolArgs(ToolName, Adjuster(Args, FileNameRef), FileNameRef),
@@ -436,7 +459,8 @@
       OverlayFileSystem(new llvm::vfs::OverlayFileSystem(std::move(BaseFS))),
       InMemoryFileSystem(new llvm::vfs::InMemoryFileSystem),
       Files(Files ? Files
-                  : new FileManager(FileSystemOptions(), OverlayFileSystem)) {
+                  : new ToolingFileManager(FileSystemOptions(),
+                                           OverlayFileSystem)) {
   OverlayFileSystem->pushOverlay(InMemoryFileSystem);
   appendArgumentsAdjuster(getClangStripOutputAdjuster());
   appendArgumentsAdjuster(getClangSyntaxOnlyAdjuster());
@@ -656,7 +680,7 @@
       new llvm::vfs::InMemoryFileSystem);
   OverlayFileSystem->pushOverlay(InMemoryFileSystem);
   llvm::IntrusiveRefCntPtr<FileManager> Files(
-      new FileManager(FileSystemOptions(), OverlayFileSystem));
+      new ToolingFileManager(FileSystemOptions(), OverlayFileSystem));
 
   ToolInvocation Invocation(
       getSyntaxOnlyToolArgs(ToolName, Adjuster(Args, FileName), FileName),