The general rule is that you cannot amend from separate returns to a joint return after the due date of the return. (Separate returns means anything other than joint, not just married filing separately.) There might be an exception to the rule if your head of household status was not valid, in other words, if you did not qualify to file as head of household. I don't know if there could be an exception because your spouse has not filed a return. If no exception applies, your spouse has to file a separate return. You should consult a tax professional to find out what you can do.

Are you sure this is correct?  Form 1040X says the opposite.  You can't file Joint to Separate after the due date, not the other way around.

@catfoodv The above answer was an old one that migrated over when the user forum changed from Answer Xchange to Real Money Talk.  And---you are right---after the filing deadline you cannot switch from married filing jointly to married filing separately, but you CAN amend from separate returns to a joint return.

Since you added to such an old thread, we cannot tell what your own circumstance is.  But if one of you filed as HOH or MFS and the other has not yet filed, wait for the return that was already filed to be fully processed before you try to amend and switch to a joint return.

When you are ready--amend the MFS return to make it it a joint return.  That ONE return will the the return for the two of you.  When you file a joint return it is only ONE return for both spouses together.

https://ttlc.intuit.com/questions/1899507-how-do-i-amend-a-separate-return-to-married-filing-jointly