Deadlocks in automated flexible manufacturing systems (FMS)is a crucial problem in production process. This paper presents an effective deadlock prevention policy for a special class of Petri nets, S3PR. Based on siphon method, a set of generalized mutual exclusion constraints (GMEC) expressed by the marking vector can be found. Then monitors based on the GMEC are added to the plant model such that the siphons in the resultant net are all invariant-controlled and no emptiable siphon is generated due to the addition of the monitors. This novel deadlock prevention policy can usually lead to a maximally permissive supervisor by adding a number of monitors and arcs, the number of monitors is decided by the number of emptiable siphon in the net system, the proposed policy can work excellently in proper size petri net system. Finally two manufacturing examples are utilized to illustrate the proposed method.