According to the IRS:
Generally, an alien in H-1B status (hereafter referred to as “H-1B alien”) will be treated as a U.S. resident for federal income tax purposes if he or she meets the Substantial Presence Test. The test is applied on a calendar year-by-calendar year basis (January 1 – December 31).
If, at the end of your tax year, you are married and one spouse is a U.S. citizen or a resident alien and the other spouse is a nonresident alien, you can choose to treat the nonresident spouse as a U.S. resident. This includes situations in which one spouse is a nonresident alien at the beginning of the tax year, but a resident alien at the end of the year, and the other spouse is a nonresident alien at the end of the year.
If you make this choice, you and your spouse are treated for income tax purposes as residents for your entire tax year. Neither you nor your spouse can claim under any tax treaty not to be a U.S. resident. You are both taxed on worldwide income. You must file a joint income tax return for the year you make the choice, but you and your spouse can file joint or separate returns in later years.
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