Recently, various-shaped coastal structures have been studied and developed. Among them, the submerged breakwater became generally known as a more effective structure than other structures, bemuse it not only serves its original function, but also has the ability to preserve the coastal environment. Most previous investigations have been focused on the wave deformation and energy dissipation due to submerged breakwater, but less interest was given to their internal properties and dynamic behavior of the seabed foundation under wave loadings. In this study, a direct numerical simulation (DNS) is newly proposed to study the dynamic interaction between a permeable submerged breakwater aver a sand seabed and nonlinear waves, including wave breaking. The accuracy of the model is checked by comparing the numerical solution with the existing experimental data related to wave $cdot$ permeable submerged breakwater $cdot$ seabed interaction, and showed fairly nice agreement between them. From the numerical results, based on the newly proposed numerical model, the properties of the wave-induced pore water pressure and the flow in the seabed foundation are studied. In relation to their internal properties, the stability oj the permeable submerged breakwater is discussed.