The key to the Chinese path to modernization lies in the modernization of science and technology, which puts forward new requirements for promoting the construction of scientific and technological powerhouse and accelerating the realization of a high-level scientific and technological self-reliance and self-improvement. However, there is still a lack of methodology and new ideology on innovation management to guide the upgrading of the overall effectiveness and efficiency of the national innovation system while promoting its transformation. Focusing on the new mission and challenges of China’s national innovation system, this study critically reviews the theoretical and practical bottlenecks of the national innovation system, the new system for mobilizing the resources nationwide and organized scientific research, putting forward the new strategic paradigm of “organized innovation” to comprehensively improve the overall effectiveness and efficiency of the national innovation system based on the ideas of holistic innovation and context-driven innovation theories. Clarify the connotation and theoretical basis of organized innovation, systematically explore its core components and typical features, further explain the operation mechanism from the perspectives of structure, process and function, and put forward practical pathways. This study provides theoretical guidance and strategic decision-making reference for promoting the overall strategic orientation of national innovation system construction from catch-up and innovation-driven to beyond catch-up and innovation-lead, adhering to the people-centered innovation road, reinforcing the central status and leading role of enterprises in innovation, improving the new national innovation system, accelerating the formation of national anticipate capability for the new-quality productivity.