This paper presents a numerical model for the simulation of solitary wave transformation around a permeable submerged breakwater. The wave-structure interaction is obtained by solving the Volume-Averaged Reynolds-Averaged Navier-Stokes governing equations (VARANS) and volume of fluid (VOF) theory. This model is applied to understand the effects of porosity, equivalent mean diameter of porous media, structure height, and structure width on the propagation of a solitary wave in the vicinity of a permeable submerged structure. The results show that solitary wave propagation around a permeable breakwater is essentially different from that around impermeable one. It is also found that the structure porosity has more impact than equivalent mean diameter on the wave transformation and flow structure. After interacting with the higher structure, the wave has smaller wave height behind the structure with a lower travelling speed. When the wave propagates over the breakwater with longer width, the wave travelling speed is obviously reduced with more wave energy dissipated inside porous structure.