The competition for limited resources can produce deadlocks in flexible manufacturing systems (FMS). Petri net is an effective way to model, analyze, and control deadlocks in FMS. Proposed by our previous work, elementary siphons are an efficient method to investigate the deadlock problems in Petri nets. An elementary siphon based deadlock prevention policy is developed in this paper. Also this research presents an analysis to show the advantages of elementary siphons in the design of liveness-enforcing Petri net supervisors. By analyzing the deadlock control problems in three different scale FMS examples, this paper shows that our policy always leads to structurally simple liveness-enforcing net supervisors. Moreover, the superiority of our approach can be clearly shown by large scale FMS.