The system deadlock problem of the flexible manufacturing system (FMS) needs to be solved urgently. Deadlocks may occur when resources are repeatedly requested by multiple working processes, where such competition causes a lack of resources, and the system cannot get into subsequent processes smoothly. In this paper, we build FMS by using a particular class of Petri Net (PN) model called a system of simple sequential processes with resources (S 3 PR) net, which features a high utilization rate of resources. When parts of resources are held by related processes and these processes wait for others to release resources to move on, a circular waiting situation occurs. Circular waiting is one of the conditions for system deadlocks occurring, where the system under this situation has a high probability of causing system deadlocks. The resources being held have to be released to break the waiting states. This paper develops a novel control transition-based deadlock recovery policy by combining graph theory and reachability graph analysis technique. The proposed approach firstly builds a subnet of the PN model called resource flow graph (RFG) and finds out all its hold and request circuits (HRCs), which may lead to a circular waiting situation. In addition, we design a new algorithm to obtain the minimal set of control transitions further. We introduce three PN models of FMS to demonstrate the proposed method. Through experimental results and comparison between related works, it is known that the proposed deadlock recovery uses fewer controllers and has the same performance.