For Illinois, if you file a joint Illinois return and one spouse is a full-year resident, both spouses must be treated as full-year residents. This means your wife's worldwide income for the entire year would be subject to Illinois tax. If you want your wife to be taxed only as a part-year resident, Illinois allows you to file as Married Filing Separately (MFS) for the state return even if you file jointly for Federal. Filing Status - IL-1040, Individual Income Tax Return
For the steps to file the separate Illinois returns, see How do I prepare a joint federal return and separate state
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