A quite great progress of the supervisory control theory for discrete event systems (DES) has been made in the past nearly twenty years, and now, automata, formal language and Petri nets become the main research tools. This paper focus on the Petri nets based supervisory control theory of DES. Firstly, we review the research results in this field, and claim that there generally exists a problem in Petri nets based supervisory control theory of DES, that is, the deadlock caused by the controller introduced to enforce the given specification occurs in the closed-loop systems, especially the deadlock occurs in the closed-loop system in which the original plant is live. Finally, a possible research direction is presented for the solution of this problem. A quite great progress of the supervisory control theory for discrete event systems (DES) has been made in the past nearly twenty years, and now, automata, formal language and Petri nets become the main research tools. This paper focus on the Petri nets based supervisory control theory of DES. that we review the research results in this field, and claim that there exists generally a problem in Petri nets based supervisory control theory of DES, that is, the deadlock caused by the controller introduced to enforce the given specification occurs in the closed-loop systems, especially the deadlock occurs in the closed-loop system where which the original plant is live. Finally, a possible research direction is presented for the solution of this problem.