Hi,
I am on H1B visa and I have been filing Federal 1040 (joint return with my wife) as a resident alien for the past 3years. Last year I moved to Wisconsin so I have to file as a part-year resident.

For Wisconsin State Tax, I am confused as to whether I have to file as a non-resident alien (in which case I do not get the standard deduction) or whether I can file as a resident alien

PS I have a SSN but my wife who is on H4 has an ITIN

Thanks

You are part year resident of Wisconsin.

If you are present in a state, then any income earned during this period, must be reported to the state.

To your resident state, you must report your worldwide income for the year.
Read: Your U.S. Tax Return: Working or Living in Two or More states (http://taxipay.blogspot.com/2008/06/working-in-two-or-more-states.html)