The new national system is an institutional arrangement that adheres to the system concept under the new development pattern. This paper uses Qian Xuesen’s system theory to understand and grasp the connotation of the open complex giant system characteristics of the new national system. Its openness determines that the institutional framework should be open and can actively adapt to external pressure. Its complexity determines the system must take precise measures and promote synergistic effects. The characteristics of giant system require the transformation of quantity energy into quality energy to stimulate the overall comparative advantage. This paper discusses how to systematize the new national system with the task of developing national strategic science and technology (S&T), and puts forward that the core of the system is to adhere to the party’s overall leadership of strategic S&T. Then, six implementation subsystems of resource planning, basic research, S&T transition, S&T talents, S&T information, and international S&T exchange and cooperation are constructed at the national strategic level.