The present study investigates numerically damping characteristics of irregular waves passing over a permeable seabeds. At first, the numerical model, which is able to consider the flow through a porous medium with inertial, laminar and turbulent resistance terms and determine the eddy viscosity with LES turbulent model, is validated by comparing with existing experimental data. And then, the numerical test on irregular wave damping over a permeable seabeds is performed in case that wave and flume conditions are changed. It is revealed from the numerical results that the more porosity and mean grain are increased, the more wave damping is increased. Also, the effect of wave period on damping of irregular waves over a permeable seabed is discussed.