In response to the limitations of two types of site selection methods based on port evaluation and operations research optimization, from the perspective of Chinese port and shipping enterprises, a model for selecting container hub ports in overseas port clusters was established, considering both the lowest total cost of logistics network and the optimal supply conditions of hub ports. The model was solved using the second-generation non-dominated sorting genetic algorithm (NSGA-Ⅱ). Taking the port cluster on the West Coast of Africa as a case study, the constructed model was applied to conduct a simulation analysis of the container hub port selection schemes under different scenarios, and the priority sequence for the construction of container hub ports within the port cluster was determined based on the hub port weighted selection probability. The results demonstrate that the model can integrate the advantages of the two site selection methods and can be solved efficiently based on the NSGA-Ⅱ algorithm, making the obtained site selection results more in line with the interests of Chinese operators. Moreover, from the perspective of China, some ports led by the Port of Tangier and the Port of Durban possess hub value among the port cluster on the West Coast of Africa.