diff --git a/src/Microsoft.DocAsCode.Build.Engine/LinkPhaseHandler.cs b/src/Microsoft.DocAsCode.Build.Engine/LinkPhaseHandler.cs
index 03c48ef9cf9..e76abee18af 100644
--- a/src/Microsoft.DocAsCode.Build.Engine/LinkPhaseHandler.cs
+++ b/src/Microsoft.DocAsCode.Build.Engine/LinkPhaseHandler.cs
@@ -150,11 +150,12 @@ private void CheckFileLink(FileModel model, HostService hostService, SaveResult
                         ToFileInSource = ((RelativePath)fileLink).RemoveWorkingFolder().ToString(),
                         FileLinkInSource = path,
                         GroupInfo = Context.GroupInfo,
+                        Href = path.UrlEncode()
                     };
-                    fli.Href = path.UrlEncode();
-                    if (Context.ApplyTemplateSettings.HrefGenerator.GenerateHref(fli) != null)
+
+                    if (Context.ApplyTemplateSettings.HrefGenerator.GenerateHref(fli) != fli.Href)
                     {
-                        return;
+                        return; // if HrefGenerator returns new href. Skip InvalidFileLink check.
                     }
                 }
                 if (result.FileLinkSources.TryGetValue(fileLink, out ImmutableList<LinkSourceInfo> list))
diff --git a/src/Microsoft.DocAsCode.Build.TableOfContents/TocDocumentProcessorBase.cs b/src/Microsoft.DocAsCode.Build.TableOfContents/TocDocumentProcessorBase.cs
index d0519359176..84f1ec5ccf5 100644
--- a/src/Microsoft.DocAsCode.Build.TableOfContents/TocDocumentProcessorBase.cs
+++ b/src/Microsoft.DocAsCode.Build.TableOfContents/TocDocumentProcessorBase.cs
@@ -158,7 +158,13 @@ private string ResolveHref(string pathToFile, string originalPathToFile, FileMod
         var fli = FileLinkInfo.Create(model.LocalPathFromRoot, model.File, path, context);
         var href = context.HrefGenerator?.GenerateHref(fli);
 
-        if (fli.ToFileInDest == null && href == null)
+        // Check href is modified by HrefGenerator or not.
+        if (href != null && href != fli.Href)
+        {
+            return UriUtility.MergeHref(href, segments);
+        }
+
+        if (fli.ToFileInDest == null)
         {
             // original path to file can be null for files generated by docfx in PreBuild
             var displayFilePath = string.IsNullOrEmpty(originalPathToFile) ? pathToFile : originalPathToFile;
@@ -167,7 +173,7 @@ private string ResolveHref(string pathToFile, string originalPathToFile, FileMod
         }
 
         // fragment and query in original href takes precedence over the one from hrefGenerator
-        return href == null ? fli.Href + segments : UriUtility.MergeHref(href, segments);
+        return fli.Href + segments;
     }
     #endregion
 }
diff --git a/test/Microsoft.DocAsCode.Build.Engine.Tests/DocumentBuilderTest.cs b/test/Microsoft.DocAsCode.Build.Engine.Tests/DocumentBuilderTest.cs
index dc45bba0c09..bf31bf0ae37 100644
--- a/test/Microsoft.DocAsCode.Build.Engine.Tests/DocumentBuilderTest.cs
+++ b/test/Microsoft.DocAsCode.Build.Engine.Tests/DocumentBuilderTest.cs
@@ -57,6 +57,7 @@ public void TestBuild()
             {
                 "# [test1](test.md#bookmark)",
                 "## [test2](test/test.md)",
+                "## [GitHub](GitHub.md?shouldBeAbbreviated=true#test)",
                 "# Api",
                 "## [Console](@System.Console)",
                 "## [ConsoleColor](xref:System.ConsoleColor)",
@@ -97,6 +98,7 @@ public void TestBuild()
                 "Test external xref with absolute URL and anchor: @str",
                 "Test invalid autolink xref: <xref:?displayProperty=fullName>",
                 "Test href generator: [GitHub](GitHub.md?shouldBeAbbreviated=true#test)",
+                "Test href generator: [Git](Git.md?shouldBeAbbreviated=true#test)",
                 "<p>",
                 "test",
             },
@@ -205,6 +207,8 @@ public void TestBuild()
                 Assert.NotNull(model[0].Items);
                 Assert.Equal("test2", model[0].Items[0].Name);
                 Assert.Equal("test/test.html", model[0].Items[0].Href);
+                Assert.Equal("GitHub", model[0].Items[1].Name);
+                Assert.Equal("GH.md?isAbbreviated=true&shouldBeAbbreviated=true#test", model[0].Items[1].Href);
                 Assert.Equal("Api", model[1].Name);
                 Assert.Null(model[1].Href);
                 Assert.NotNull(model[1].Items);
@@ -213,7 +217,7 @@ public void TestBuild()
                 Assert.Equal("ConsoleColor", model[1].Items[1].Name);
                 Assert.Equal("../System.ConsoleColor.csyml", model[1].Items[1].Href);
             }
-
+            
             {
                 // check conceptual.
                 var conceptualOutputPath = Path.Combine(_outputFolder, Path.ChangeExtension(conceptualFile, ".html"));
@@ -251,7 +255,8 @@ public void TestBuild()
                         "Test invalid xref with attribute: <xref href=\"invalid\" fullname=\"Foo&lt;T&gt;\"></xref>",
                         $"Test external xref with absolute URL and anchor: <xref href=\"str\" data-throw-if-not-resolved=\"False\" data-raw-source=\"@str\" sourcefile=\"{_inputFolder}/test.md\" sourcestartlinenumber=\"30\"></xref>",
                         $"Test invalid autolink xref: <xref href=\"?displayProperty=fullName\" data-throw-if-not-resolved=\"True\" data-raw-source=\"&lt;xref:?displayProperty=fullName&gt;\" sourcefile=\"{_inputFolder}/test.md\" sourcestartlinenumber=\"31\"></xref>",
-                        $"Test href generator: <a href=\"GitHub.md?shouldBeAbbreviated=true#test\" sourcefile=\"{_inputFolder}/test.md\" sourcestartlinenumber=\"32\">GitHub</a></p>",
+                        $"Test href generator: <a href=\"GitHub.md?shouldBeAbbreviated=true#test\" sourcefile=\"{_inputFolder}/test.md\" sourcestartlinenumber=\"32\">GitHub</a>",
+                        $"Test href generator: <a href=\"Git.md?shouldBeAbbreviated=true#test\" sourcefile=\"{_inputFolder}/test.md\" sourcestartlinenumber=\"33\">Git</a></p>",
                         "<p>",
                         @"test",
                         "</p>"),
@@ -284,7 +289,8 @@ public void TestBuild()
                         "Test invalid xref with attribute: <span class=\"xref\">Foo&lt;T&gt;</span>",
                         "Test external xref with absolute URL and anchor: <a class=\"xref\" href=\"https://docs.python.org/3.5/library/stdtypes.html#str\">str</a>",
                         "Test invalid autolink xref: &lt;xref:?displayProperty=fullName&gt;",
-                        "Test href generator: <a href=\"GH.md?isAbbreviated=true&shouldBeAbbreviated=true#test\">GitHub</a></p>",
+                        "Test href generator: <a href=\"GH.md?isAbbreviated=true&shouldBeAbbreviated=true#test\">GitHub</a>",
+                        "Test href generator: <a href=\"Git.md?shouldBeAbbreviated=true#test\">Git</a></p>",
                         "<p>",
                         "test",
                         "</p>"),