The Job-Shop problems considering material transit time and machine set-up time were studied. During the optimization and calculation, the material transit time and the influences on the Job-Shop scheduling were taken into account. Subsequently, the solution method was provided and the Job-Shop scheduling problem was solved using hybrid PSO algorithm combining GA and SA. Finally, the analysis and calculation of interaction between material transit time, machining time and machine set-up time was carried out by the simulation based on real conditions. The results show that the proposed method considering the machine set-up time and material transit time is more feasible and realistic than the scheduling which appends the material machining time directly.