Recently, in the context of “The Belt and Road” Initiative, the China Railway Express, which has a high volume and spans a long distance has greatly facilitated the construction of international freight transport corridors between developed and developing countries. To ensure sustainable development, this paper introduces an optimization problem of a container distribution organization scheme for the China Railway Express resulting from the major existing problems arising in railway port stations, which is a special and crucial link in transportation organization of the China Railway Express. The problem of a long dwell time of inbound trains is typically concerned with the operation process in railway port stations. Taking various real-world influencing factors of efficiency into account, this paper formulates a distribution organization optimization model to minimize the total container-hours of inbound China Railway Express at Alataw Pass railway station. Subsequently, a solution method based on the main idea of a genetic algorithm is developed to solve the problem, and two examples of different modes of transportation organization are given for validating the effectiveness of the model. Finally, we compare the results between two modes under different orders of magnitude according to the characteristics of sustainability to discuss the possible change and development of the China Railway Express in the future.