Aiming at effect of perforated caisson on mean wave overtopping, based on the general wharf project of a certain port area in China, the paper analyzes and compares the empirical formula calculation method about mean wave overtopping of vertical and perforated caisson, and also makes a comparison between the empirical formula calculation results and physical section model test results .The results of empirical formula show that mean wave overtopping ratio of perforated caisson and vertical caisson is 25%～50%,and the results of physical section model test is 30%～82%.The study shows that perforated caisson could reduce mean wave overtopping effectively. And the results of empirical formula suggested by domestic scholars are even more similar to those of physical section model test.