Aiming at the forbidden state problem of Petri nets with uncontrollable transitions, a controller synthesis method based on integer linear programming is proposed, which is suitable for any ordinary Petri nets model. Firstly, according to the structural characteristics of Petri nets, a set of constraint conditions that all uncontrollable transitions should satisfy is constructed. Secondly, the given linear constraints are converted into admissible linear constraints by solving the integer linear programming problem. Finally, the invariant method of the library is used to design the controller and integrate the converted constraints into the Petri net. The experimental results show that the proposed method is simple and efficient, and can be used as a reference for the forbidden state monitoring in the actual automatic manufacturing system.