Wave is one of the most common dynamic factors in marine engineering. This is the major affecting factor in the design of structures and coastal engineering that wave affect the structure or the coast, so there are many topics about wave absorbing issues. In this paper, FLOW-3D modeling is implemented for wave interaction with porous structures, and comparing with experiment. This is very different between the results of models using the proposed method by the FLOW-3D User Manual to set drag coefficients of porous media and the results of experiments. Therefore, to discuss the setting drag coefficients of porous media is one of this research project. Configuration of this study, four different types of porous structures to explore the interaction with wave, the major categories: single, double and three-tier (two forms). FLOW-3D simulations of wave boundary in this article is to simulate the wave plate to manufacture wave, FLOW-3D simulations of wave with the previous studies are different with its built-in wave boundary. The results of simulation compare with experiment, and obtain water depth data both of them, and then programmatically wave analysis explore the differences between simulation and experiment. The simulation results show that stroke set by the analog wave board need to reduce 10 percent of the original settings, and the simulation results are similar to experiment results. The differences between simulation and experiment are smaller when porous media parameter ¡¥b¡¦ setting formula adjust to 0.03/D ( D is the particle diameter)and parameter ¡¥a¡¦ setting formula changeless. Reducing wave of the four porous structures relate to the wave period. The wave period is bigger and more difficult to wave absorption, and the reflectivity is proportional to wave period.