In order to optimize hydropower projects’ emergency processes and evaluate emergency response capability, the models and methods of system performance analysis have been proposed according to the theory of Petri nets. First, the model of events in emergency processes was established by abstracting the emergency response process chains. Then, based on the isomorphic characteristics between Petri nets and Markov chains, the state set that may arise in the emergency response system was set up, and thus isomorphic Markov chains could be developed. Finally, the performance analysis of the emergency response system could be made by calculating the average number of markers in various places in different linkage systems, the utilization of transitions and average execution time and so on. A hydropower project in the Yalong River was taken as an example, the analysis results of performance index show that some measures should be taken to improve the relatively time-consuming process of the public assistance emergency response procedures, and summarize the evaluation of emergency systems and post-emergency links, which can provide a reference for the emergency management to improve the operation efficiency of the entire system.