Abstract: In the flexible manufacturing system, a reasonable production scheduling can shorten the completion time of each processing task and improve the utilization rate of equipment. In order to solve the complex job shop scheduling problem in the flexible manufacturing system, the number of overdue jobs, total overdue time, comprehensive load rate of machine tool, maximum load rate of machine tool and job completion time are taken as the performance indicators of scheduling algorithm. The genetic algorithm is used to find the optimal scheduling scheme. The chromosomes are designed as process gene chains and equipment gene chains, and the diversity of chromosomes and the robustness of chromosomes to scheduling problems are improved through crossing, mutation, selection and other processes. By adjusting the relevant parameters of the algorithm, the influences of different parameter settings on the performance indicators of each scheduling algorithm are studied. This study provides a reference for the design and optimization of scheduling algorithm based on the genetic algorithm.