Abstract: The national science and technology security system is not only a core component of the national security framework, but also a critical foundational pillar for building a leading technological nation. In this paper, the differences between the U.S. and China’s science and technology security systems were compared in terms of development goals, organizational structures, priority tasks, and institutional mechanisms. Then, the international competitive landscape and domestic technological development challenges was analyzed. Based on universal principles and practical logic, a forward-looking framework for China’s science and technology security system was outlined. Suggestions were made concerning the following four aspects: strengthening the indigenous innovation system for critical and core technologies, establishing an end-to-end risk monitoring system, optimizing a dynamic national security governance system, and consolidating the U.S.–China security consultation and cooperation mechanism. The modular combination method used in this paper not only provides a flexible and multidimensional analytical perspective for comparing the U.S. and China’s science and technology security systems, revealing their internal mechanisms and external linkages, but also offers new theoretical support and practical insights for optimizing China’s science and technology security system.