for example. I can set break point at plugins files, since they are all php files. phpstorm can listen those files. but it can not track the .htm files. I am pretty like it can also help me stop at those break point in theme files. Is there any solutions to help me on this issues? Appreciate.

I'm not sure that's possible. The only way I can think of to put breakpoints on those would be to set them on the Twig compiler in the background, but then it might break thousands of times, and not be particularly useful.