The theory of thermodynamic entropy is applied for reference to solve the basic problems of supply chain management science and knowledge innovation of supply chain enterprises. As for entropy, only thermodynamic entropy, statistical physical entropy and information entropy have been recognized, so management entropy is defined as the generalization of entropy. According to the similarity between state change of management system and that of the thermodynamics system, the revelation of the microscopic mechanism of entropy essence by statistical physical entropy, and the foundation that information entropy is regarded as the generalization of entropy by scholars, it is concluded that management entropy exists and has the same properties as thermodynamic entropy. For instance, it becomes a measure of the degree of chaos and disorder of a system and the time vector of the management system. A knowledge innovation sharing model of supply chain enterprises is constructed based on the thermodynamic entropy theory, the process of knowledge sharing in supply chain is analyzed, and the possibility of knowledge sharing among supply chain enterprises from the point of view of game theory is discussed. The principal-agent theory is used to analyze the incentive strategy to promote knowledge sharing in supply chain, and the model of knowledge sharing in supply chain is established.