Over 30 years of reform and development in China have witnessed the establishment of non-governmental education, which is closely linked with its governance system. At present and in the future, the innovation of governance system of non-governmental education centers and will center on three core topics, namely classification management, government functions and the corporation system. First, exploring a scientific approach to classification management is the most important system arrangement to strengthen the legal basis and consummate the top-level system design for non-governmental education. Second, transforming the government functions is the major incentive to achieve good governing and stimulate the intrinsic vitality for non-governmental schools. Third, improving the corporate governance is key to the micro self-government and stable operations for non-governmental schools. With the deepening of comprehensive reform in education, the institutional environment of non-governmental education in China will be further improved.