Material supply isthe basic guarantee for the large ship sailing to ocean. In order to improve the efficiency of the supply of the large ship, the support of materials handling system is needed. According to the typical material handling system of the large ship, with the material handlings time shortest as the decision goal and the handling sequence as the decision variable, the analysis and construction of the model for optimizing the systems operation is given in this paper. The improved genetic algorithm is put forward. The specific model is also given and its proved that the analysis and modeling method in this paper can effectively improve the efficiency of the material handling of the large ships.