Goals reasoning and management of pilot is a key issue to monitor pilot’s behavior and intention. Traditional modeling methods are based on scenarios or situations, such methods will cause the covering problem due to redundancy and are incapable of depicting interactions among various goals and plans of pilot.Petri net integrated with belief, desire and intention(BDI) theory(BDI Petri net) is designed to solve this problem. Focusing on the BDI theory, goal states of agent are discussed firstly. Belief, desire and intention are modeled by places and transitions based on the Petri net theory. In order to simplify the network, colored token is introduced to depict various states of belief, and the hierarchy transition is applied to model the intention, together with tokens’ flow demonstrating the interaction among various goals and relationship among belief, desire and intention. A search and rescue mission is used to validate the proposed method and the result indicates that the model can be used to monitor goals and behaviors of pilots. Goals reasoning and management of pilot is a key issue to monitor pilot’s behavior and intention. Traditional modeling methods are based on scenarios or situations, such methods will cause the covering problem due to redundancy and are incapable of depicting interactions among various goals and plans of pilot Focusing on the BDI theory, goal states of agent are discussed preceded. Belief, desire and intention are modeled by places and transition order based on the Petri net theory. In order to simplify the network, colored token is introduced to depict various states of belief, and hierarchy transition is applied to model the intention, together with tokens’ flow demonstrating the interaction among various goals and relationship among belief, desire and intention. A search and rescue mission is used to validate the proposed method and the result indicates that the model ca n be used to monitor goals and behaviors of pilots.