A three-dimensional model test about Suizhong district of Huludao harbor is conducted and the enhanced Boussinesq equations are used to simulate the wave conditions of different layout schemes in the harbor. Influences of breakwater’s structure type,breakwater gap’s direction and width,the channel，and structures of the harbor boundaries are studied. The results show that selecting proper harbor layout types will diminish the wave height in harbor effectively and provide a scientific guidance for the optimization of general harbor layout planning. Besides,the limitations of physical model test and math model test are discussed to provide a method of combining both to research harbor planning.