In order to solve the vessel traffic organization problem in restricted two-way channel and improve the efficiency of port navigation, a mixed-integer planning model were established to solve the application requirements, taking into account the pilot, tugboat, tide, safety distance and traffic conflict factors in one-way and two-way channel, and taking the minimum of the total waiting time of the vessels as the optimization objective. Considering the characteristics of the model, an improved differential evolution (IDE) algorithm was proposed to solve the problem. After experiments with different number of vessels, the scheduling results were compared with the results of FCFS and other algorithms to verify that the model and algorithms can effectively provide vessel traffic organization solutions for restrictive two-way channel.