In view of the general layout design problem of the coastal wharf with strong sediment transport rate under long-period swells，taking a supporting boat wharf project in the Benin Bay as an example，the island breakwater scheme is adopted. The rationality of the general layout design of the island breakwater is verified by using wave numerical model test and sediment scouring and silting numerical model test，so as to solve the general layout problem. A preliminary calculation of the ship’s vertical displacement is carried out based on the Japanese code，and the hydrodynamic finite element analysis method is used to compare and verify the calculation results of the code，which solves the problem of channel design water depth under the condition of long-period waves. The results show that：1）Under the conditions of long-period wave and strong sediment transport rate，the wave protection determines the layout conditions such as the harbor entrance orientation and breakwater axis. 2）The distance between the breakwater and the surf zone and the water depth of the approach channel are both the controlling factors to determine the plan position of the breakwater，which must be reasonably justified and calculated. 3）The Japanese code calculation method is more suitable for the design of channel water depth under the condition of long period waves，and it is recommended to be used in similar projects.