Accurate estimation and prediction of wave deformation around a submerged breakwater are researched. Characteristics of changes of the wave profile and energy spectrum at different relatively depth of submergence and different relatively crest width of submerged breakwater under regular wave passing over a submerged breakwater installed on the 1/20 sloping bed are investigated by a two-layer, depth-integrated Boussinesq model. The proposed numerical model is examined by comparison with the experimental results. The numerical result shows that the wave profile may become more asymmetry when wave propagates over breakwater. Wave energy may rapidly decrease at the breakwater because turbulent dissipation increases and the energy in lower harmonics are transferred into higher harmonics. The results show the lower the relative depth of submergence or wider the relative crest width of submerged breakwater is, the more asymmetry the wave profile is and the more the relative fundamental energy decreases.