I married in 2019 to my wife who was working as an Au Pair program in the United States (same state MA as we both now live and work) while she was still on a J1 visa. She received her green card the same year in 2019 (November). She made $4,100.00 as an Au Pair from January 2019 to May 2019, but was paid in cash. The last two tax years, she filed a 1040NR and paid between $90 - $200 in taxes between 2017 and 2018 due to deductions she was allowed to claim (such as airfare and visa costs, phone bills for work, etc.) When enter her income in TurbuTax, our expected refund drops by roughly $1,100, which appears to be taxing her near a 25% flat rate. Comparitively, on an IRS.gov website form for filing 1040NR, it estimated the tax liability to be $400, or around 10%. I am using the TurboTax Deluxe version.
First of all, the IRS Form 1040 NR you use is only for non-residents and the TurboTax program is only designed for US citizens and residents. These are two completely different tax forms with two distinct sets of tax laws. The rules for claiming certain tax credits and deductions, exemptions and tax rates are not the same.
If your spouse has had a J-1 visa for 2017 and 2018, she is considered as non-resident for those two years and required to file a Form 1040-NR. Starting from January, 1st 2019, if she has stayed physically for more than 183 days within the US regardless of her visa status, she is a US resident for tax purposes.
If you are a US citizen or resident, you both can file jointly on a normal US return Form 1040 just like other Americans by using one of the TurboTax programs. Please note that the TurboTax program only available for US citizens or residents to file, not non-residents.
To read more information between residents and nonresident, click here: Differences
I hope this helps.