Abstract: Technological innovation is a strategic support for improving national competitiveness and guaranteeing national security. Our country has achieved a series of major breakthroughs such as the "two bombs and one satellite" with a nationwide system, laying the cornerstone for national security and striving for prosperity, and has accumulated meaningful experience. At present, under major changes unseen in a century, our country is facing unprecedented strategic opportunities, risks and challenges. In the face of the arduousness and complexity of achieving national goals, we must make a better use of the key role of the new nationwide system on overcoming the "stuck neck" problem and achieving high-level scientific and technological self-reliance. Therefore, based on the comparative analysis of the development of science and technology in key areas at home and abroad, we conduct dialectical research on the nationwide system of science and technology innovation. We analyzed the nature of the nationwide science and technology innovation system, extracted common key elements and country characteristics, and focused on exploring the advantages and possible implementation risks of the nationwide science and technology innovation system and the contradictions that need to be properly handled to build a new nationwide system of science and technology innovation. At Last, we promote that in order to achieve the greatest contribution to major scientific and technological innovations by the new national system, it is necessary to seek advantages and avoid disadvantages in the dialectical balance of advantages and disadvantages so as to make the most advantageous strategic choices and overall planning, promote institutional innovation and system integration innovation, and comprehensively improve the capacity of science, technology and innovation governance.