For responsiveness, in the Petri nets theory framework deadlock prevention policies based elementary siphons control are often utilized to deal with deadlocks caused by the sharing of resources in flexible manufacturing system (FMS) which is developing the theory of efficient strict minimal siphons of an S 3 PR. Analyzer of Petri net models and their P-invariant analysis, and deadlock control are presented as tools for modelling, efficiency structure analysis, control, and investigation of the FMSs when different policies can be implemented for the deadlock prevention. We are to show an effective deadlock prevention policy of a special class of Petri nets namely elementary siphons. As well, both structural analysis and reachability graph analysis and simulation are used for analysis and control of Petri nets. This work is successfully applied Petri nets to deadlock analysis using the concept of elementary siphons, for design of supervisors of some supervisory control problems of FMS and simulation of Petri net tool with MATLAB.