Abstract: China's national system of scientific and technological innovation has experienced the establishment and development of the planned economy period and the adaptive adjustment after the reform and opening up period, and has initially explored the allocation of resources and the organizational mode suitable for the socialist market economy. As the new development of the national system in the new era, a new national system of science and technology innovation need to inherit the advantages of concentrating resources to accomplish large undertakings, and give better play to the synergy of the government's major scientific and technological innovation organizers and market incentives. The key essence is to focus on the needs of key and core technological breakthroughs, and to give new connotations to the four aspects of overall planning and allocation of national strategic resources, improving the level of organization and coordination in scientific and technological breakthroughs, strengthening the guarantee of basic scientific and technological breakthroughs, and stimulating the vitality and efficiency of the national system. In terms of overall distribution and allocation of national strategic resources, it will build a vertical and horizontal policy mix system and promote the integrated, overall allocation of resources in key areas; In terms of making scientific and technological breakthroughs more organized and coordinated, it will develop and expand a number of government-industry-industry-university-research-application-application innovation coalitions for the tasks and objectives of major scientific and engineering innovations that are important to the national strategy. It will improve the national innovation ecosystem, improve the supply of public science and technology infrastructure, foster and develop national innovation institutions, and form a long-term mechanism for tackling key and core technologies. In order to enhance the vitality and efficiency of the national system, it should make proper adjustments to the role of the government, promote the in-depth integration of the national system with the market mechanism, and make greater use of the incentive and constraint role of market competition to stimulate the creativity of scientific and technological personnel and teams.