Wave energy is a kind of renewable and clean energy. When waves meet the breakwaters, wave energy reflection will happen. In this paper, the modified mild slope equation for waves propagating over the permeable seabed is introduced, and the finite difference model to solve the equation is set up. The accuracy and applicability of the model is verified with Zeng et al’s analytical solution for wave reflection by the rectangular Bragg breakwaters on the impermeable seabed. Furthermore, in case of a permeable seabed, the effects of the seabed permeability, the bar width, the bar number and the submergence of the bars on wave reflection coefficient, as well as the difference with the case of an impermeable seabed, is studies in details. The results show the reflection coefficient of the Bragg resonant reflection increases with the increase in the bar number, but decreases with the increase in the seabed permeability and the submergence of the bars. When the bar number increases from 1 to 8, the Bragg resonance reflection coefficient increases from 0.146 to 0.772. When the permeability parameter of the seabed increases from 0.005 s to 0.03 s, the coefficient decreases from 0.403 to 0.347. When the bar submergence increases from 0.5 to 0.875, the coefficient decreases from 0.842 to 0.195. Moreover, there exists a particular value of the bar width, that is half of the distance between two adjacent rectangular bars that maximizes the wave energy reflection.