Deadlock in flexible manufacturing systems (FMS) which refers to the stop state of job flow in the system can be commonly occurred in operating FMS. This state mainly due to bad movements of jobs and commonly job routings should be avoided to maximize the utilization of high-capital resources in this study, the deadlock generated from the conflict between flow objects competing to occupy space resources in FMS is investigated. Capacity Designated Directed Graph (CDG) is constructed to represent the space resources and flow object routings. From the characteristics of CDG, an algorithm for the detection of the deadlock possibility is proposed. Finally two deadlock avoidance rule are proposed and implemented in the control on Automated Guided Vehicle system in an FMS.