In the situation you described, you could choose to file a joint Federal return and your spouse could file a separate Illinois return.
According to the Illinois Department of Revenue:
If you file a joint federal return and one spouse is a full-year Illinois resident while the other is a part-year resident or a nonresident (e.g., military personnel), you may choose to file "married filing separately." Do not recalculate any items on your federal return.
Instead, you must divide each item of income and deduction shown on your joint federal return between your separate Illinois returns following the Allocation Worksheet in the Form IL-1040 Instructions.
Each state has its own rules regarding this topic. For example, Arizona allows couples to file separately even if they filed a joint federal return, whereas Colorado does not. California doesn't allow it either, with the exception of active-duty military and certain nonresidents.
You can use TurboTax Online to file separate state returns, but we recommend you use the TurboTax Desktop software version to do this because you'll only need to pay for one TurboTax product (you can file up to five returns).
See this help article for more information.
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