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.Europe advocates that railways should take more transportation volumes, which requires an increase in the service level of the multimodal transport chain and increases the market share of railway transportation in terms of medium-and long-distance freight. Specifically, before the end of 2020, they aim to establish a framework system for the management and payment information system of the EU multimodal transport; before 2030, they will require 30% of road freights to be transferred to rails and waterways, and will reach 50% by 2050 [2]. In 2017, the proportions of rail-sea intermodal transportation were 36% in Duis, 39% in Hamburg and 47% in Bremen.However, the development of multimodal transport is different in China. Although it has been more than ten years of promoting the mode of rail-water transportation in China, due to insufficient transportation capacity of the railway system and other reasons, the implementation of rail-water transportation has been slow.With the continuous advancement of the "Thirteenth Five-Year Plan" and the "Belt and Road" strategy, China has established the notion that lucid waters and lush mountains are invaluable assets and acted with resolve and intensity as never before to strengthen environmental protection. At the same time, an aim of energy consumption per unit of GDP (Gross National Product) falling more than 20% has been set. As the pillar industry of the country, the transportation industry will play a vital role in the process.That's why China is entering a g...