In view of the production quality management of filter rods in the manufacturing and execution process of cigarette enterprises, this paper analyzes the necessity of implementing the manufacturing execution system (MES) in the production process of filter rods. In this paper, the filter rod quality system of cigarette enterprise based on MES is fully studied, and the constructive information management system demand analysis, cigarette quality control process, system function module design, implementation and test effect are given. This paper utilizes the Fuzzy analytic hierarchy process to find the optimal system for processing the manufacturing of cigarette. The implementation of MSE based filter rod quality information management system for a cigarette enterprise ensures the quality control in the cigarette production process. Through visualization, real-time and dynamic way, the information management of cigarette production is completed, which greatly improves the quality of cigarette enterprise manufacturing process.