Inland waterway transportation is an important part of the comprehensive transportation system of sustainable development, and it is also a way of transportation which is restricted by natural conditions greatly. In recent years, the problems of insufficient traffic capacity of The Three Gorges become prominent due to the increasing in the number of ships. And the ship’s detention caused by gale, frog, accident and one-way traffic in dry season has occurred, which not only increased the pressure of the navigable waterway but also seriously affected the safety of shipping. Based on the different types of ships, the Arena software was used to simulate the ship traffic flow. The paper analyzed the traffic congestion propagation and dissipation rule of the ship under different navigation control methods, and provided decision reference for the navigation management department to formulate the relevant navigation control strategy.