If you live in a different state from your spouse, but want to use the married filing jointly status on your taxes, rest assured your separate residences won't automatically disqualify you. However, your ability to file a joint return will depend on a number of factors, such as how your spouse chooses to file and whether you're legally separated.
TL;DR (Too Long; Didn't Read)
Even if you live in a different state than your spouse there are no rules prohibiting you from filing a joint tax return.
You Must be "Considered Married"
For the purpose of determining your eligibility to file a joint return with your spouse, the Internal Revenue Service requires that you be “considered married” on the last day of the tax year. There are three ways to be considered married: You are legally married and live together as husband and wife; your state recognizes a legal common law marriage despite your separate residences; or you're legally married but live separately and a legal separation agreement doesn't exist. If you and your spouse fall under any of these three situations, you satisfy the requirements to file a joint return. Therefore, you can file joint returns every tax year that you live in separate states as long as you don't become legally separated.
Consent to File a Joint Return
If you're considered married, the only other requirement to filing a joint return is your spouse's consent. However, the IRS will be satisfied that both of you consent to the joint filing if the tax return includes both your signatures. However, the fact you live in different states will not exempt you from the signature requirement. As a result, the IRS suggests you have the tax return prepared enough in advance of the deadline so that you have time to obtain your spouse's signature, or if e-filing, for your spouse to obtain an e-file PIN.
When You're "Considered Unmarried"
Since you and your spouse live in different states, one of you may be eligible to file as head of household if you're “considered unmarried.” A person who is legally married can be considered unmarried for tax purposes if he lives apart from his spouse for the last six months of the tax year and paid more than half the cost to maintain a home that is the main home for a child, stepchild or foster child who can be claimed as a dependent. However, if one of you files as head of household, the other must file a separate return using the married filing separately status.
Filing Status Implications
As the IRS notes, it's usually beneficial for married couples to file jointly since it generally results in a lower overall tax bill compared with filing two separate returns. Moreover, your standard deduction is double that of a single taxpayer and it may be easier to satisfy the eligibility requirements for other tax benefits. However, if one spouse chooses to file as head of household, that option is still better than both spouses using the married filing separately status since it comes with a larger standard deduction and lower tax rates.