diff --git a/xmake/rules/linker/link_scripts/xmake.lua b/xmake/rules/linker/link_scripts/xmake.lua
index fdd7149885..34bbc3f4fd 100644
--- a/xmake/rules/linker/link_scripts/xmake.lua
+++ b/xmake/rules/linker/link_scripts/xmake.lua
@@ -42,8 +42,10 @@ rule("linker.link_scripts")
         if target:has_tool("ld", "gcc", "gxx", "clang", "clangxx") or
             target:has_tool("sh", "gcc", "gxx", "clang", "clangxx") then
             target:add(target:is_shared() and "shflags" or "ldflags", "-T " .. scriptfile, {force = true})
+            target:data_add("linkdepfiles", scriptfile)
         elseif target:has_tool("ld", "ld") or target:has_tool("sh", "ld") then
             target:add(target:is_shared() and "shflags" or "ldflags", "-T " .. scriptfile, {force = true})
+            target:data_add("linkdepfiles", scriptfile)
         end
     end)
 
diff --git a/xmake/rules/platform/windows/def/xmake.lua b/xmake/rules/platform/windows/def/xmake.lua
index 5d1957b0bd..9bdcdc8747 100644
--- a/xmake/rules/platform/windows/def/xmake.lua
+++ b/xmake/rules/platform/windows/def/xmake.lua
@@ -38,8 +38,8 @@ rule("platform.windows.def")
                     flag = "/def:" .. flag
                 end
                 -- https://github.com/xmake-io/xmake/pull/4901
-                target:data_add("linkdepfiles", sourcefile)
                 target:add("shflags", flag, {force = true})
+                target:data_add("linkdepfiles", sourcefile)
                 break;
             end
         end
diff --git a/xmake/rules/platform/windows/manifest/xmake.lua b/xmake/rules/platform/windows/manifest/xmake.lua
index 8d24ced973..6bde53a3d5 100644
--- a/xmake/rules/platform/windows/manifest/xmake.lua
+++ b/xmake/rules/platform/windows/manifest/xmake.lua
@@ -34,6 +34,7 @@ rule("platform.windows.manifest")
                 for _, sourcefile in ipairs(sourcebatch.sourcefiles) do
                     target:add("ldflags", "/manifestinput:" .. path.translate(sourcefile), {force = true})
                     target:add("shflags", "/manifestinput:" .. path.translate(sourcefile), {force = true})
+                    target:data_add("linkdepfiles", sourcefile)
                     manifest = true
                     local content = io.readfile(sourcefile)
                     if content then