Ma’ao harbor of Ningbo-Zhoushan port locates in the central waters of Zhoushan, and Guanmen throat section channel is the main restrictive channel of Ma’ao harbor. Due to the limit of both sides’ reefs and the overhead line, the channel has complicated flow and a sharp turning angle, and thus is one of the most complex channel in Zhoushan area. By reference to foreign norms and the experience of Zhoushan-area’s navigation, the layout of the reef explosion is optimized by mathematical modeling, ship simulation and real ship testing, and the navigation time of ships passing through the throat section of Guanmen is optimized by the measured current data,and the navigational ability is improved by rational using of the overhead line’s catenary form. This paper gives a design method of channel in complex island waters, and can provide reference for similar projects.