Filing federal return jointly but state separately?

Yes, your husband will have to file a New York Income Tax Return if he has New York-sourced income..  Per New York State Department of Taxation and Fiance, separate returns are required for some married taxpayers who filed a joint federal return.  

Depending on the details of your circumstances: "If one of you was a New York State resident and the other was a nonresident or part-year resident, you must each file a separate New York return. The resident must use Form IT-201. The nonresident or part-year resident, if required to file a New York State return, must use Form IT-203. However, if you both choose to file a joint New York State return, use Form IT-201."

Per West Virginia's Tax Division: "Married couples with different periods of residency must file separate state income tax returns".

Every state is different. It depends on which state you live in. Some states allow you to file a joint return with your nonresident spouse, and in others you can't.  Some states may prefer a separate return for each spouse for state purposes.

The most important factor in determining the kind of move you made and how it affects your state income tax returns is your intent. States want to know:

• Did you intend to make a permanent move? (Whatever your intent, you need to back it up by your actions.)
• How much time did you live in the other state?
• Did your immediate family move to the new state with you?

Answer all of the questions and followup prompts in TurboTax and the program will select the proper state income tax returns for you to file.

Click here for additional information on New York Taxes for Residents and NonResidents.

Click here for information from West Virginia's Tax Division.

Click here for Multiple States tax returns.