Abstract: China's innovation and development has entered a new stage of self-reliance and self-improvement, and it is urgent to build a new system. Different from the traditional public institutions and new R&D institutions with enterprises as the main body, it is of great significance to build a new type of institute with collaborative innovation of government, society and enterprises and flexible mechanism for realizing the breakthrough of neck technology and common technology in key fields and promoting the integration of science, technology and economy. Based on the "four natures" (public welfare, economy, sociality and innovation) of the new Institute, this paper constructs a two-tier governance theoretical framework, which is parallel to the decentralization of the system and the support of the market-oriented mechanism. It is verified by the successful practice of Jiangsu Industry Research Institute, that is, the effectiveness and necessity of the two-tier governance model.