To modernize China’s governance system and capacity for governance and to implement the strategy of innovation-driven development, it is necessary to improve the innovation system and accelerate the innovation of technology system. From the perspective of capital diversity, the innovation of innovation system and technology system needs to make efforts on the basis of respecting the optimal allocation of capital elements, so as to build a more efficient and optimized supply-side structure and promote economic development. Innovation has a great traction effect on enterprises. The improvement of total factor productivity depends on the innovation activities and efficiency improvement of enterprises. Innovators are distributed among multiple participants. The reasons should be clarified and their effective origin distribution should be improved. To recognize the social nature of innovation, under complete market competition, respect objective laws, avoid the inefficiency of innovation in different situations, and maximize social surplus value. In the innovation of the entire technological system, there is a strong complementarity between the various systems (the principle of complementation), and the interaction of the various systems based on the principle of complementation can form the innovation of the technological system with diverse capital.