Based on the consideration of the loading and unloading of twin 40’ quay cranes， the stowage of 20’ and 40’ dry containers and reefer containers， and the influence of ship hatch cover， a mixed integer programming model is established to solve the multi-port main master bay plan problem， whose aim is to minimize the total loading and unloading times of container crane on the route. The bin packing algorithm with over-sized items is designed based on heuristic rules to obtain the stowage plans of 20’ and 40’ containers in the cabin in mixed loading strategy and non-mixed loading strategy. It is found that the non-mixed loading strategy can effectively improve the total loading and unloading efficiency and the stowage model and algorithm can optimize the stowage plan， which generally improves the efficiency by at least 24.5% compared with common quay cranes under equal conditions.