To optimize the wavesheltered conditions in the harbour, adjusting the direction of the boundary line between the port and the waterway, optimizing the adjustment plan base on the original design scheme, three connection schemes are arranged. The wave field in the marina precinct of the three layout schemes were calculated with MIKE21-BW mathematical model.The design wave elements of each scheme and the pre-quay wave conditions are obtained and the result is that the sheltered condition of thefirst programme is the worst, and the sheltered condition of the third programme is the best plan. The reason is that the slope of the third plan is relatively large and the angle of the incident wave is small, and the wave of the slope can be further spread beyond the embankment. It show that the sheltered conditions of the waters in the harbour can be optimized by adjusting the boundary conditions of the water in the harbour. And when the angle between the water boundary and the incident is smaller, the sheltered condition is better than others. Calculating the dredging quantity of the three layout schemes with Civil 3D,combined with the actual investment of engineering and other factors, the second plan is proposed as the recommended plan for this project.