Based on the operation situation of railway logistics center under electronic commerce environment, the railway electrical business logistics center was divided into 8 function areas: receiving area, storage area, picking, packing, shipping, returns, equipment area and office area. The systematic layout planning (SLP) was reformed quantitatively, the method of mathematical modeling was added, and the factors of logistics influence were analyzed more scientifically. According to the improved SLP method, the logistics factors and non-logistics factors affecting the railway e-commerce logistics center were analyzed, and the comprehensive relational table was constructed. Under the constraints of no overlap of functional zones, no more than the planned scope of functional areas, a certain range of length-width ratios of railways, no occupancy of areas dedicated to railways, entrances and exits of parks, etc., the objective function of minimizing the material handling cost, maximizing interval integrated relationship, and minimizing the cost of land reform in the park was established, and then the objective function was processed to get the normalized single objective function. Through improved genetic algorithm, a scientific and reasonable layout plan was obtained. Finally, a practical example shows that the layout method in this paper is scientific and reasonable.