The purpose of our study is to develop numerical simulation to investigate the toughness of tsunami disaster countermeasures. Moving Particle Semi-implicit (MPS) method was used in the simulation. The wall boundary was applied polygon-wall boundary instead of particle-wall boundary. As the result, we suggested that MPS used the polygon-wall boundary is possible to calculate with high accuracy fluid dynamics than particle-wall boundary. Furthermore, in the simulation of tsunami overflowing the breakwater, the presented method was able to reproduce the vortexes generating by tsunami overflowing the breakwater. The values of velocity also were in agreement with that of the model experiments. It was obvious that the roll-up flow accompanied with the vortexes is due to scouring of the mound.