To solve the problems of insufficient navigation capacity, it is recommended to expand the old ship locks, as result, some lock chambers become irregular. In order to improve the utilization efficiency of chamber area, the different methods of ship arrangement were designed and optimized. The simulation models of traffic flow, ship scheduling and lock chamber arrangement were built, and a lock simulation prototype system was designed to verify it. The Hongjiang Lock’s expansion project was taken as an example to test and evaluate the ship arrangement optimization methods of a non-rectangular chamber by using the developing simulation system. This study has theoretical and practical value for the non-rectangular chamber arrangement.