With the high-speed development of industrialization process and the Internet e-commerce in China, the number of the fast cargoes is increasing. The transportation demands of customer should be provided in a convenient and efficient way. However, compared to road and aviation, railway express freight network is lagging in China, the market share is relatively low, and the service is still in a low level. The operation scheme of railway express freight train can improve the railway efficiency. This paper studies the railway express freight train schemes on several related questions. They are as follows: (1) We analyze the factors of operating express freight train. (2) Based on the assumption of the shortest path for the flow of traffic, the operation scheme of express freight railways is optimized by establishing a multitarget model with making the largest railway revenue and the largest satisfaction of cargo owner. (3) The multitarget model is proposed to be converted into a single-target model. It is the case of carrying out the operation scheme in the four logistics node cities of the southwest China. The following conclusions are taken: (1) The choice method of the flow path is generally analyzed by heuristic method, which is more accurate. (2) We establish a multiobjective optimization model on the base of getting the maximum of transport revenue and satisfying the cargo owner’s demand.