In this paper we proposed a model that the deformation of the submerged rubble mound breakwaters composed with materials of various size, induced by wave action, can be computed. The water particle kinematics by waves in porous mound structure are computed by CADMAS-SURF, then the deformation of structure is computed using DEM module. To investigate the interaction of wave and sectional deformation of structures, analysis is accomplished by two steps. Analysis at the first step is executed with incipient mound. And analysis at the second step is executed with deformed mound by wave action. Furthermore, behaviors of materials are influenced by various properties such as the contact stiffness and the friction angle. Therefore, in order to present the behavior of the element caused by various properties, computations are accomplished with random coefficients by using the Monte Carlo simulation.