To solve the coordinate control problem in the automated guided vehicle system(AGVS), a method based on directed graph to design control programs automatically is proposed. Firstly, the directed graph model based on regional control is constructed by the structure of the AGVS. Then, the concept of extended dangerous region is defined under the condition of partial observation. A method for estimating the number of vehicles in a dangerous region is given, and a control strategy for collision prevention of the guide path is proposed. Finally, two conditions of deadlocks in AGVS are discussed, and a corresponding deadlock control method is given. The effectiveness of the proposed methods is verified by several simulation experiments.