My son (MI resident) received 1099-NEC for his internship while studying in IL. Now graduated and working in IL, W-2 employee. How should he file state taxes?

He will want to file Part-Time Michigan and Illinois.  For Michigan, he will report 1099-NEC.  For Illinois, he will have nonresident Illinois income (1099-NEC because he was working in Illinois while a resident of Michigan) and resident Illinois income for the W2.  If he can identify the date he received interest and/or dividends, he can report to the state where he was a resident.  

Thank you!  As far as 'resident' status goes on a tax filing purpose, would it be your own call (whether or not you call IL a new domicile)?  1099-NEC has his IL address on it.  (And W-2 as well)

No, it's not your call whether to call IL the domicile state. Your son is definitely a resident once he gets a job in IL. 

• He probably changed his drivers license and other documents to read IL.

However, when he received the 1099-NEC, he was a resident of MI. You even stated in your description that your son was a MI resident.

• He probably had a MI drivers license and other documents to read MI.

 It doesn't matter that the 1099-NEC has his IL mailing address. The mailing address does not automatically make you an IL resident. 

Please see the TurboTax FAQ What is my state residency status? 

• Generally, you're a resident of a state if you don't intend to be there temporarily. It's where home is—where you come back to after being away on vacation, on a business trip, or at school. Think of it as your permanent home.

Thanks, very helpful!