The permeable breakwater with baffle is a new structural type.It can conduct water exchange and protect the harbor at the same time,and the realization of these functions depends on the reasonable design of baffle’s depth.Based on the theoretical calculation,we carry out the comparative analysis of the results of engineering wave mathematical model and physical model,and obtain the influence of different water entry depth of wave baffle on the wave cover,wave height distribution and wave overtopping in the harbor.The results show that the increase of water entry depth of wave baffle outside the wharf decreases the wave height at the rear berths of the wharf,increases the horizontal force on wharf structure,increases wave overtopping,decreases operating days and enhances protection of the harbor.