For the problems of encountering and overtaking in the process of in-and-out port of ships in the container terminals with two-way channel, a new ship dispatching optimization algorithm focusing on the service rules was proposed. Firstly, the realistic constraints of two-way channel and the safety regulations of port night sailing were considered at the same time. Then, a mixed integer programming model with the goal of minimizing the total waiting time of ships in the terminal was constructed to obtain the optimal in-and-out port sequence of ships. Finally, the branch-cut algorithm with embedded polymerization strategy was designed to solve the model. The numerical experimental results show that, the average relative deviation between the result of the branch-cut algorithm using embedded polymerization strategy and the lower bound is 2.59%. At the same time, compared with the objective function values obtained by the simulated annealing algorithm and quantum differential evolution algorithm, the objective function values obtained by the proposed branch-cut algorithm are reduced by 23.56% and 17.17% respectively, which verifies the effectiveness of the proposed algorithm. The influences of different safe time intervals of ship arriving the port and ship type proportions were compared in the sensitivity analysis of the scheme obtained by the proposed algorithm, providing the decision and support for ship dispatching optimization in container terminals with two-way channel.