The current schedule of ports and berths still remains in the single-port multi-berth, while multi-port and multi-berth integrated scheduling based on the container port cluster can achieve the optimal allocation of ports resources, reduce the time in port and improve the resource utilization rate, and at the same time, the optimal transportation cost of the ship company has been taken into account. Therefore, the multi-objective non-linear programming model for multi-port and multi-berth integrated scheduling system was constructed with certain assumptions as premises. Then, a heuristic algorithm for the model was designed according to the specific structure of the model's decision-making space. Finally, the numerical calculation was performed in order to verify the effectiveness and stability of the algorithm. It shows that the decision model is practical and the algorithm is valid.