This paper studies the flexible job shop scheduling problem under the condition that with parallel processes. In this paper, we analyses the characteristics of the process parallelism in the job shop scheduling problem, puts forward the concept of parallel efficiency, establishes the flexible job shop scheduling model with parallel processes based on the objective criteria of minimizing the makespan, and designs the model solution algorithm based on genetic algorithm. The feasibility of the scheduling model and the effectiveness of the algorithm are verified by simulation experiments. The parameters of process parallel rate are compared and analyzed. The experimental results show that it is effective to improve the scheduling efficiency by improving the parallelism of the process route.