Supply chain optimization configuration contributes to the improvement and development of enterprise business application system. This paper takes the supply chain of manufacturing enterprises as the research object and analyzes the economic benefits of supply chain optimization of manufacturing enterprises. Aiming at the current development environment of enterprises, it puts forward the necessity of the development of enterprise supply chain flexibility, and establishes the overall supply chain flexibility model that contains the supply flexibility of the supply chain, the manufacturing flexibility and the distribution flexibility of the distributors. Simplify the total cost model of supply chain and establish the demand-driven supply chain optimization model. Analyze and validate the parameter settings of the improved particle swarm algorithm, and obtain the operating efficiency of the improved particle swarm algorithm with the changes of ordering cycle and inventory capacity. Combined with the sample enterprises, analyze the financial savings of each link after supply chain optimization. Further measurements show that after supply chain optimization of Company R, the saving percentage is 10.24%, and the annual saving amount is 562,807 yuan, with obvious economic benefits.