Adopting the basic Petri net, the sub-systems models of the manufacturing logistics system were established. The logistics system modeling method with O-O colored timed Petri net (OCTPN) was put forward. This model method did not only have the figure and symbol description mode which was coincident with human thinking mode, but also avoided the model complexity that caused by the system complexity. At the same time, the manufacturing and logistics system has been modeled, the hierarchy model including the manufacturing process model and the logistics system model was established. Took a logistics planning in the automobile rear bridge plant as the example, the system has been modeled and analyzed with OCTPN method. WITNESS has been used in computer-aided model and simulation to design and optimize the production logistics system in the H1 automobile rear bridge plant.