With the continuous advancement of globalization and informatization, logistics business has achieved unprecedented development, but at the same time, it also faces many challenges. In order to improve the quality and efficiency of logistics business processes, it is necessary to conduct in-depth analysis and optimization. This study is based on Petri nets to model and analyze logistics business processes. Through the analysis of logistics business process, a method of logistics business process modeling based on Petri net is proposed. Firstly, the logistics business process is decomposed and the relationships between each process are determined. A Petri net model of the logistics business process is constructed. Then, through model simulation and analysis, bottleneck areas and factors affecting process efficiency are identified, and optimization plans are proposed. The proportion of railway transportation is the highest, accounting for 40%, so optimizing railway transportation routes can significantly reduce the logistics delivery time.The experimental results show that the use of Petri nets for logistics business process modeling is feasible and practical, and can provide guidance and reference for the optimization of logistics business processes.