The dimensions of the breakwater and the direction of the entrance have great influences on wave height distribution，berthing stability and sediment in the harbor basin，and the reasonable arrangement of the breakwater and the entrance is the key factor for the construction of the fishing port. Based on the results of mathematical models of wave，tidal current and sediment of the engineering case，we carry out a comparative analysis and optimization design of the general layout，particularly the entrance layout of a first-grade fishing port in Hainan from angles including the shielding effect，safety of ship operation，and berthing stability，etc. to provide a guidance for the design and construction of the fishing port breakwater.