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The integrated scheduling problem of the container handling system in container terminals is presented as a mixed integer programming model with the predefined operation constraints, sequence depended setup time and interference constraints for quay cranes. Based on the characteristics of container terminal operations, a heuristic algorithm is developed to solve this problem under the condition that container handling system is dealing with discharging or loading jobs only. Furthermore, the lower bound of the problem is suggested. And the numerical experiments show the algorithm effective and efficient comparing to lower bound, particularly for large scale problems.