If you and your spouse have different MA residency periods, Massachusetts requires you to use the filing status of Married Filing Separately on the MA return (you may still file a joint Federal return). This website: https://www.mass.gov/service-details/learn-about-filing-status-on-massachusetts-personal-income-tax contains the following:
Taxpayers who are legally married as of the last day of the tax year can file as married filing separately.
If married taxpayers have a Massachusetts residency tax year that begins and ends on different days, they must file married filing separately, assuming each spouse is required to file. (Italics added)
If you do choose to file a joint Federal return while being required to file separate MA returns, this FAQ provides instruction on how to do so: https://ttlc.intuit.com/replies/3301995
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