> What I specifically need is that, let emacs treat another
> file as the "~/.emacs" file.
>
> This file should behaves EXACTLY as "~/.emacs" except that
> they have different file name.
>
> That means, if I click Options -> Save Options, emacs
> would write changes to this specific file.
No, the last two sentences do not say the same thing.
If you want what you say in the second sentence, then use option `custome-file',
as I said before. Then just put (load-file custom-file) in your .emacs.
This way, you still have your .emacs file for any non-Customize customizations
you might want to make. And you can choose at which point in your .emacs you
want to load the customizations provided by Customize, by placing (load-file
custom-file) wherever you want.
Please read the Emacs manual about `custom-file':
C-h r
i custom-file