To minimize the total time in harbor and improve customer satisfaction, different levels of punishment for the delay completion tasks and the deviation from the optimal berthing position are considered. To make full use of quay crane resources, dynamic scheduling of quay crane is taken into account and combined with continuous berth allocation simultaneously. An integer programming model is established to minimize the penalty costs of delay completion tasks, deviating from the optimal berthing location and quay crane movement. Berthing schedule and specific quay crane assignment plan can be gained. Experiments are carried out to verify the model, which show that the proposed approach can improve the efficiency of container terminals and the satisfaction of ship companies.