The modeling and simulation issues of the flexible manufacturing system under Just-in-Time environment is addressed in this paper. A typical flexible manufacturing system has been used as the study case, and its Petri nets model with Kanban has been presented. Since bottleneck or hunger resources in the manufacturing system usually have bad influence on the production process, more attentions were paid to the bottleneck identification and digestion in support of the proposed modeling and simulation mechanism in this paper. The machine utilization, under the premise of meeting custom needs just-in-time, is used as the main measure, while the trigger priority and the kanban numbers are two main adjusted artifices. Therewith, a large number of numerical simulations are investigated and detail discussions are proposed further. The simulation results show that the proposed Petri nets based modeling technique, as while as the bottleneck identification and digestion strategies, are feasible and effective.