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In order to reduce the detention time of ships in the port, make full use of port resources and optimize port services. This paper analyzes the factors that affect the efficiency of the dispatching of ships entering and leaving the port, and studies the coordinated dispatching of multiple ship types and multiple berth types. Based on the proposed hypothesis, with the minimum total scheduling time and the minimum waiting time as the optimization goals, a coordinated scheduling model for berth allocation and channel was established. Based on the NSGA-II algorithm, a multi-objective optimization genetic algorithm suitable for solving the model of berth allocation and channel coordination scheduling is designed. By testing the intensive ship entry and exit data in a short period of time, the solution efficiency and stability of the algorithm in this paper are better than those of the NSGA-II algorithm, and it is more suitable for solving the optimization problem of berth allocation and channel coordination scheduling.