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No, it will not affect his return. One of the reasons to file separately is to not co-join your income, etc. Your balance due is yours alone.

However, there are some disadvantages to filing separately.

 Pros

Here are some instances where it might be better to file separately:

•  If you or your spouse owe back taxes or child support, the IRS may keep some or all of your refund
• You or your spouse may have a combined income that raises your student loan payments
• Your spouse might not be totally honest in their reporting. (Happens often during a divorce.)
• You or your spouse may have a lot more medical expense than the other (and a significantly lower income)
• You and/or your spouse have a lot of medical expenses (especially if one spouse has a lower significantly lower income)
• You and your spouse both have similarly high incomes.

Cons

Although there is no one answer since every situation is different, generally filing jointly will give you a bigger refund or less taxes due. When you file separately, your tax rate is higher and you won't be able to claim:

• Student loan interest deduction

• Education benefits
• Earned Income Credit (EIC)
• Child and Dependent Care Credit (usually)
• Adoption Credit (usually)

• The same benefit married filing jointly couples get for personal exemptions, itemized deductions, the Child Tax Credit, and capital losses (all of these deductions are reduced by half)
• Itemized deductions if your spouse has already claimed the standard deduction, or the other way around.

On top of that, if you live in the community property states of Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington, or Wisconsin, you have to deal with community property allocations and adjustments, which adds extra work and complexity to your tax preparation chore.