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This paper aims to use optimization method to solve the Berth-Quay Crane Allocation Problem. The objective used here is to minimize the total stevedoring time and the total operational cost. In order to solve the problem in reasonable time, the multi-objective Particle Swarm Optimization (PSO) method is designed. Five instances with 30, 40, 50, 60, 70 ships are used for testing the model and PSO. The result of experimental computations indicate that the algorithm is effective and the model can get the optimal trade-off solution between time and cost. Compared with the single-objective model, the multi-objective model is more beneficial to the whole shipping system.