The IRS is very clear that taxpayers, including married couples, have only one primary residence—which the agency refers to as the “main home.” Your main home is always the residence where you ordinarily live most of the time. ... There are, however, tax deductions the IRS offers that cover the expenses on up to two homes.
It's perfectly legal to be married filing jointly with separate residences, as long as your marital status conforms to the IRS definition of “married.” Many married couples live in separate homes because of life's circumstances or their personal choices.
The key phrase in that last paragraph is primary residence. Second homes typically do not qualify for this exclusion. However, it's worth mentioning that the IRS defines the term primary residence as somewhere that you lived full-time for at least two of the five years preceding the sale.
Please check out this IRS Publication on the sale of your residence.
Sale of Residence
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