The purpose of this research is to solve the problems of unreasonable layout of the production plant, disorder of the logistics process, and unbalanced production line in discrete manufacturing plants. By analyzing the production process and characteristics, the timed Petri net model is constructed according to the function and connection of each production unit, which is then used to generate a FlexSim simulation model of the production plant logistics system with a simulation software. Therewith the FlexSim simulation model is used to simulate the original layout of the plant, and to analyse the simulation data synthetically to put forward an improvement strategy. Combined with the use of the systematic layout planning method to analyze the overall layout of the plant and logistics relations, we infer the relevant drawings between the production units and determine the improved layout of the facilities. Finally, by comparing the before and after improvement simulation results, it is verified that the combination of timed Petri nets and systematic layout planning is effective to ameliorate the layout of the plant facilities and the logistics system. This method makes up for the factors that traditional methods have not considered, achieves the goal of reducing the cross circuitous route of the plant and the idle rate of equipment, and improving the efficiency of production.