For federal tax, you almost always pay more in tax if you're married and file separately (MFS). Even though your husband was staying in Michigan while working there, he was still an Illinois resident. You should file a joint federal tax return and a joint Illinois tax return. You will also have to file a Joint Michigan tax return. Illinois and Michigan have reciprocal agreements with each other. Residents of reciprocal states working in Michigan do not have to pay Michigan tax on salaries or wages earned in Michigan. You will have to file a Schedule NR along with an MI-1040 to receive a refund of Michigan tax withheld.
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