Abstract:Based on innovative governance theory, this paper analyzes the innovation measures and governance characteristics of Japan’s new type of scientific research institution system. It shows that the new system, which has replaced innovation management with innovative governance and shifted orientation from supply-push to demand-driven, is in line with the characteristics and rules of R&D activities being carried out by Japan's National Research and Development Agency. It is helpful not only to government to put in place mechanisms that encourage collaborative innovation relying on research institutes as agencies partner, but also to institutions to accelerate the commercialization of innovative technology by integrating the combined efforts of industry and academia. As such, the innovation governance practices of Japan's research system are useful for us to improving a modern scientific research institution governance system with Chinese characteristics and encouraging research institutions play an intermediary role of a bridge in the process of industry-university-research collaborative innovation, in order to solve the problems with the application of advances in science and technology and find out the solution to the principal–agent problem occurred in the process of innovation incentives.