As the technological iteration and industrial restructuring accelerate gradually, the integration of industrial chain and innovation chain has changed from chain-type integration to chain-network integration, forming a complex system. Based on the connection and entirety, the connotation, structure and dynamic factors of the "two chains" integration are analyzed. In the "two-chain" integration system, integration is the key point, value co-creation is the foundation, and overall efficiency improvement is the goal. According to system theory and social network theory, the structural characteristics of the integration of "two chains" are analyzed from the aspects of internal and external based on node-chain-network three levels. Finally, it is proposed to take the five driving factors as breakthroughs, including core nodes, intermediaries, key part of core technologies, cooperative trust and mechanism innovation, and strive to improve the driving force, matching degree, innovation, synergy and guarantee of the integration of "two chains".