In the design of breakwaters, on the basis of guaranteeing the stability, optimum types of protection are chosen to reduce the overtopping and thus decrease the construction cost. The roughness and permeability coefficients are introduced in most recent calculations of overtopping, illustrating the effect of protection on the overtopping rate. However, this influence can be variable according to different locations for the protection types.Therefore a modeling experiment is conducted in present study to investigate the effect of flat and shoulder types on the rate of overtopping under irregular wave conditions.When different protections are used to reduce the overtopping, not only the roughness and permeability, but also the positions of the protection should be considered.The effect will be better when the protection is putted in the swash area, which can be a reference for the design of breakwaters.