My main research advisor refuses to give me a letter (to help for apply US physics program). What should I do?
Yes, it might look a bit weird, but you don't have control over that. And he is giving you good advice that he shouldn't write you a letter. Not every advisor is willing to be so honest.
But, I don't think it is an absolute block to your plans. Find others to write you strong letters and (US perspective) you should be ok.
What you need are letters from people who can confidently and honestly predict your future success based on their experiences with you. This advisor is not that person.
And FWIW, it is his problem, not a problem with your work mode. And no admissions committee should make any decisions based on guesses or suppositions. They should take your materials as they stand.