Flat organization structure is an important means to improve the management efficiency of railway freight car production enterprises. This paper uses the structure entropy model to analyze the order degree of the traditional organization and the flat organization structure, and calculates the time-efficient entropy sum of the two organizational structures. It is found that the flat entropy and quality entropy of the flat organizational structure are higher than those of the traditional organizational structure. The actual operation shows that the flat organizational structure can be restructured by rebuilding the salary distribution system, integrating relevant functions, improving the production rhythm, and reducing the production employment, which can solve the problem of imbalance in salary distribution among enterprises and some overlapping management functions among departments and workshops, thus reducing manufacturing costs.