In order to more effectively analyze the performance of logistics emergency rescue system, based on analyzing the characteristics and main functions of the Petri net and its advantage of describing asynchronous concurrent random image system, this paper introduces stochastic Petri net modeling method to establish emergency system model on the basis of serious natural disasters or emergencies, and analyzes the performance. Firstly, according to the emergency rescue system of logistics flow chart, the Petri net model is built, and through the analysis of accessibility, activity and safety, the validity of the model is verified; Secondly, the Markov chain is constructed using the characteristics of isostructuralism with the Markov stochastic process, the linear equations is established, and a numerical example is introduced, reflecting the problems of the system through the quantitative analysis of main performance indexes. Finally, some suggestions are put forward about the problems. On the one hand, this modeling can vividly describe the sequential and asynchronous concurrent relationships between the processes; on the other hand, its mature performance analysis method can effectively explore the key links which have significant impacts on the operational efficiency of the system. The system analysis theory provides a feasible method for the analysis of system flow, and the proposal provides a theoretical basis for the optimization of the entire emergency logistics rescue system.