You are partially correct. In general, Illinois requires you to use the same filing status as on your federal return. However, according to the 2025 Form IL-1040 Instructions: 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, file “married filing separately.”
If you are using TurboTax Online, you should switch to TurboTax Desktop. You will need to prepare three separate returns: one Married Filing Joint return and two mock Married Filing Separately federal returns - one for each separate Illinois state return. You will be able to e-file the joint return, along with your New Jersey state return, but you will need to mail your Illinois returns.
The reason you need to switch to TurboTax Desktop is so you can create the joint return, and then make two copies of that return (by "saving as" and using a different file name). You can create as many tax returns in TurboTax Desktop as you want. After creating a joint federal return and making a copy for mock MFS return, you will delete all of your spouse's information, change the filing status to MFS, and if you already prepared it, deleting the New Jersey return. You can do the same thing for the other spouse.
To switch from TurboTax Online to TurobTax Desktop see the following article: How do I switch from TurboTax Online to TurboTax Desktop?
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