The Third Plenary Session of the 20th Central Committee of the Communist Party of China made systematic arrangements for further comprehensively deepening reform, emphasizing the construction of a system and mechanism that supports comprehensive innovation, promoting the integrated reform of the education, science and technology, and talent systems, and improving the new national system, and enhancing the overall efficiency of the national innovation system. There is an inherent logical connection between the construction of university disciplines and the development of the national innovation system. Empowering the national innovation system is an intrinsic requirement for the construction of university disciplines. To improve the overall efficiency of the national innovation system, it is necessary to perfect the construction of interdisciplinary fields that meet the strategic needs of the country and the corresponding talent cultivation models. From the perspective of the transformation of knowledge production model, exploring how the construction of university disciplines can empower the national innovation system and finding its promotion path are of significant theoretical and practical importance for accelerating the development of new productive forces. At present, the transformation of knowledge production model has given rise to innovative characteristics such as innovation-driven, high-quality elements, openness and inclusiveness, and element synergy, revealing the logical coupling in university discipline construction empowering the national innovation system, including subject integration, value efficiency, cross-border collaboration, and systematic interaction. However, in the practice of university discipline construction, there are still barriers in terms of organizational logic, value logic, cultural logic, and dynamic logic, which affect its empowerment for the development of the national innovation system. To overcome these barriers, it is possible to strengthen the organization of scientific and technological innovation, promote the integration of disciplines and industries, build a transdisciplinary culture, and promote the integration of disciplines and scientific and technological talents, thereby enhancing the core driving force, industrial innovation capacity, cultural soft power, and development support power for the development of new productive forces. Therefore, the construction of university disciplines should not only focus on the deepening of basic research but also pay attention to the development of applied research and interdisciplinary research to adapt to the rapidly changing technological trends and market demands, playing a crucial role in empowering the overall efficiency of the national innovation system. In the future, universities should continue to deepen the reform of discipline construction and strengthen the interaction and integration with the national innovation system to make greater contributions to promoting the progress of science and technology and economic and social development.