IRS Rules for the Tax Deduction of Bonuses. The Internal Revenue Service regards bonuses as supplemental wages, which are not regular wages. If you choose to reward your employees for their hard work with a bonus incentive, the payment is taxed according to how it is made.ubtract 1.000 from 0.3065 to get 0.6935.Then, divide the bonus amount of $1,000 by the decimal amount of 0.6935 to arrive at $1,441.96. You would pay the tax cost of $441.96 and the employee would receive $1,000.