In view of the current problems of complex and changeable business processes and high management difficulty in the logistics industry, this paper introduces a logistics business process modeling and analysis method based on Petri net. Firstly, the various links of the logistics business process were systematically sorted out and converted into the basic elements of Petri nets, including positions, transitions and arcs. Then, the key nodes and possible bottlenecks in the logistics process were modeled and analyzed by using the concurrency and synchronization characteristics of Petri nets. Finally, by introducing the time Petri net, the model was further optimized to achieve an accurate description of the time constraints in the logistics process. The experimental results show that the optimization scheme based on Petri nets significantly reduces the execution time of the logistics process. In the baseline model, the total execution time of the logistics process is 115 m, and after the introduction of time Petri net optimization, the total execution time is reduced to 90 m, and the optimized process saves 25 m. In addition, the resource utilization rate after optimization has also been significantly improved, especially in the transportation and distribution links, from 55% to 75% and 80% to 90% respectively. In the above data conclusion, model optimization based on Petri net can effectively improve the efficiency of logistics process and provide scientific decision support for logistics enterprises.