For the us In general you’ll get a bigger deduction if you file married jointly than separately. However individual circumstances vary and there might be a reason to file separately. You’ll have to ask a professional or do both types of returns and see if one gives slightly better conditions. If both of you are already filing us returns anyway then jointly is usually best but I can’t say for sure. If he wasn’t filing in the us then it might be better not to do it this way though. The thing that will matter most for Japan is how much they earn and whether one is a dependent of the other or whether you are both earning and basically separate entities. I’m not expert on Japan though. And my advice is not professional advice.