Hi jingfang,
In the Project_Settings of project in workspace, inside the Linker_Files should have the .ld file like below:

The tool should automatically coppy the .ld file from C:\NXP\S32DS.3.5_2\S32DS\software\PlatformSDK_S32K3\RTD\Platform_TS_T40D34M30I0R0\build_files\gcc and link it in DS. Not manually coppy it.
Please help me to check again.
Is it possible if you can share your project here? You can export it and share the zip file here.

And you're using S32K RTD 4.0.0 is that correct? I want to check it directly for help you.
Thank you,
Nam.