At present, the manufacturing operation management system of enterprise has some problems in production logistics, such as low efficiency, high cost and unreasonable logistics scheduling. To solve this problem, the research considers the optimization of manufacturing operation management from the Angle of logistics intelligence. According to the correlation between product and order demand and genetic algorithm, the logistics distribution path and collaborative optimization are realized. Then the logistics function is introduced into the framework of the manufacturing operation management system, and the management system is designed. Therefore, a manufacturing operation management system based on genetic algorithm is constructed. The experimental results show that after the application of the management system proposed in the study, the cost of product material distribution is reduced by 25.36%, and the distribution time of single product is reduced by 10.35%. In addition, the single task response time of the proposed management system in operation is only 0.28s. This indicates that the management system constructed by the research institute has significantly improved the efficiency of manufacturing operations of enterprises. It reduces the cost of material distribution and shortens the time of product distribution.