To solve the problem of state space explosion caused by formal modeling methods, a simulation model and performance evaluation method for high performance cluster based on Petri net are proposed. Firstly, the system structure of high performance cluster is analyzed and a general model is constructed. Then the sub-models for task generation and scheduling are built respectively for cluster system. Finally, according to the characteristics of different kinds of tasks, the corresponding task processing models of different tasks are designed by coloring the Petri net. The simulation results show that the proposed model could effectively evaluate the effects of key parameters on cluster performance.