As the petri net modeling has good visibility and excellent dynamic expressiveness, the paper introduces a methodology of utilizing Petri Net to perform reliability modeling on complex system. Through simulating the formed Petri Net model of the complex system by means of the Monte Carlo Simulation，which has formed a whole theory on reliability analyze, and the computation results can be required finally. Eventually, the case of wire flight control system is applied, the simulated result of which proves the validity and accuracy of the above methodology. Thus, the reliability analyze methodology based on Petri Nets can be applied to the complex aircraft system efficiently.