The initial resource allocation optimization problem of automatic manufacturing system is to complete the preset production task under the premise of the minimum use of initial resource. To solve this problem, a method based on labeled Petri nets and integer linear programming is proposed. First, according to the structural characteristics of labeled Petri nets, the constraint relationship between the proposed task and the initial resource is given, and the initial resource allocation optimization problem is abstracted into an integer linear programming problem. Secondly, the software Lingo is used to solve the integer linear programming problem. Finally, an example is given to verify the proposed method. The experimental results show that the proposed method is simple and efficient, which can be used for reference in the initial resource allocation of the actual automatic manufacturing system.