The problem of wave partial/full reflection and transmission by wave-permeable structure is approached by solving the shape-related function with focus on the understanding of wave attenuation.2D depth-averaged Boussinesq type wave equations are given with new damping item in simulating the nonlinear wave transmission through wave-permeable structure.1D wave equation is examined to give the analytical expression of the absorbing coefficient, and is compared with laboratory data in flume to calibrate the coefficients, and the expression is applied directly in modified Boussinesq type equations.Compared with wave basin data for various incident wave conditions,the accurate predictions of combined diffraction-refraction effects in simulating nonlinear wave going through wave-permeable breakwater in the engineering application can be obtained.It shows that wave-permeable breakwaters with proper absorbing effects can be used as an effective altative to massive gravity breakwaters in reduction of wave transmission in shallow water.