Considering the importance and complexity of scheduling to modern manufacturing systems, this paper puts forward a hybrid heuristic scheduling algorithm for flexible manufacturing system (FMS) based on Petri net (PN). Specifically, the PN modelling and scheduling algorithm of the FMS were discussed in details, and the hybrid heuristic scheduling algorithm was proposed based on the reachability graph of PN model. On this basis, a PN-based strategy for discrete event system (DES) modelling was developed, and applied to simulate the scheduling of a production line of shock absorbers. The results show that the FMS scheduling can be simulated effectively through the combination between extended PN and FlexSim.