Abstract: As an innovative mechanism for industrial chain governance with Chinese characteristics, the “Chain Leader System” provides an institutional solution to bridge the disconnection between scientific and industrial innovation and accelerate the development of new quality productive forces. In this study, data on industrial chains covered by the “Chain Leader System” across Chinese prefecture-level cities were manually collected and were linked with composite scores measuring the deep integration of scientific and industrial innovation in 278 cities from 2012 to 2021. Employing a multi-period difference-in-differences model, the policy’s impact on this integration was empirically examined. Results demonstrate that the “Chain Leader System” significantly enhances deep integration between scientific and industrial innovation—a finding robust to multiple sensitivity checks. Mechanism analysis reveals that the policy primarily drives integration through innovation factor empowerment and fiscal leverage effects, while a favorable business environment positively moderates its implementation pathway. Heterogeneity analysis indicates stronger policy efficacy in eastern regions, larger cities, and those with higher economic agglomeration or entrepreneurial vitality.