Compared with the traditional national system, the new characteristics of the new national system are facing a new era background, based on a new institutional foundation,shouldering new historical tasks, and based on new development conditions. The implementation of the new national system needs to follow the complementary logic of a proactive government and an effective market,the dialectical logic of independent innovation and open innovation,the unified logic of problem orientation and free exploration, and the mutually reinforcing logic of basic research and applied research. Five key mechanisms were constructed to promote the implementation of the new national system, namely the strategic guidance policy traction mechanism,the market determined resource allocation mechanism,the continuous support mechanism for basic research,the linkage mechanism of education and technology talents,and the coordination mechanism of strategic scientific and technological forces.