It depends. It is optional for a married couple to file jointly or separately. While joint filing is usually a more tax advantaged status, it is not always the case.
However, what you may be seeing is the system calculating the tax on just one of you. It is possible that filing separate does reduce your individual tax due (or refund), but, when you combine the two filings (you filing separately and him fililing separately) the combined amount owed may be more than if you file joint.
Still it is your choice to file joint or separate, and this FAQ goes into what some of the differences are to each: https://ttlc.intuit.com/replies/3288477
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