Nowadays, many kinds of flexible manufacturing systems are used to process many complex manufacturing works due to their machine flexibility and routing flexibility. However, such competition (i.e. robots and machines) for shared resources by concurrent job processes can lead to the problem of a system deadlock. In existing researches, almost experts adopted place-based as controllers to solve the deadlock problems of flexible manufacturing systems whatever the concept of siphons or the reachability graph method are used. Among them, only the reachability graph ones can obtain maximally permissive live states. In this article, the authors try to propose one novel transition-based deadlock prevention concept to solve flexible manufacturing system’s deadlock problem. In addition, two algorithms are developed to support above concept. The experimental results indicate that the proposed policy not only can obtain maximally permissive controllers but also recover all original deadlock markings.