It has been proven that exploring how to achieve an efficient transportation system is a crucial component of every sustainable transportation study. Rail-water intermodal transportation is recognized as one of the future transportation methods for being efficient, economical and environmentally friendly. To improve the efficiency, reduce transportation costs and maximize the resource utilization of outbound intermodal container transportation, based on the relationship between the container central station and the port station in the actual problems, the organization of railway container transportation was studied. A multi-objective optimization model was established in order to minimize the total cost in the process of transportation, which means maximizing the resource utilization and ensuring it is environmentally friendly. Additionally, an improved genetic algorithm (GA) was developed to solve the model. The calculation results of the model are obtained by the simulation calculation. The comparison with the conventional fixed axis transportation organization method proves that the model and algorithm can reduce costs by up to 24.57%. The result also shows that the container transport organization should be tried to satisfy the direct loading and discharging condition of “train-ship,” meanwhile reducing the storage time at the high toll central station. In conclusion, the model and algorithm are feasible and effective. Due to the universality of the model, it can be easily used and generalized in or out of China.
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