Abstract: This study is grounded in the crucial context of accelerating the construction of Chinese modernization. The key to Chinese modernization lies in the modernization of science and technology (S&T). How to better serve the goal of S&T modernization has long been a central research issue in the field of macro-level S&T governance. Numerous policies have been introduced focusing on the reform of the S&T system, the development of the national innovation system (NIS), and the modernization of science, technology and innovation (STI) governance. They reflect the shifting priorities of macro-level S&T management across different historical periods, all ultimately aimed at achieving S&T modernization. However, in the process of policy formulation, the boundaries among these three concepts are often ambiguous and frequently conflated, which has led to confusion in macro-level S&T governance practices. Theoretically, S&T system reform, innovation system construction, and STI governance all represent institutional arrangements and transformations targeted at different actors. Yet, how STI governance bridges these disparate frameworks, and whether it can enrich the theoretical architecture of macro-level S&T management remains insufficiently explored. This paper analyzes academic literature and policy documents to explore pathways for theoretical integration among S&T system reform, innovation system construction, and STI governance, aiming to clarify the theoretical and practical evolution of national macro-level S&T management in the Chinese context. By combining qualitative methods and social network analysis, it summarizes the practical processes and theoretical developments of China’s S&T system reform, NIS construction, and STI governance. Specifically, it systematically reviews the theoretical connotations and policy objectives of S&T system reform, NIS, and STI governance, highlighting both their distinct features and commonalities. On this basis, the paper proposes a theoretical framework that links these three domains, providing a reference for policy formulation in macro-level S&T management. The study reveals that, first, the distinctiveness of S&T system reform, NIS construction, and STI governance is manifested in terms of theoretical connotations, policy practices, and research topics. Second, the key research themes in these areas converge around “the integration of S&T with the economy,” “commercialization of S&T outcomes,” “innovation ecosystem,” “indigenous innovation,” “innovation culture,” and “the China-specific national innovation system.” Finally, Considering the staged and evolutionary characteristics of Chinese modernization, S&T system reform, NIS construction, and STI governance exhibit theoretical convergence. These three systems together constitute an integrated framework centered on S&T innovation. The key actors—government, industry, academia, and research—are shared across all three systems. The NIS focuses on the substance of S&T innovation, S&T system reform emphasizes institutional and regulatory transformation, while STI governance serves as the bridge linking the two concepts. The importance of STI governance has become increasingly prominent in the new era. Based on the integrated framework, this study proposes three core propositions: (1) enhancing the effectiveness of NIS is the consistent goal of macro-level S&T governance in China. (2) accelerating S&T system reform and advancing the modernization of the STI governance are two key instruments to achieve this goal. (3) the essence of macro-level S&T governance lies in reconciling endogenous institutional transformation with exogenous institutional learning, for which the modernization of the STI governance system serves as an effective pathway.