From the perspective of scientific and technological system reform, this paper takes non-financial listed companies in Shanghai and Shenzhen A-share markets from 2013 to 2023 as the research sample, and uses a multi-period DID model to investigate the impact of the “Enlisting and Leading” system on enterprise innovation performance and its mechanism. The results show that the “Enlisting and Leading” system positively promotes the quantity and quality of enterprise innovation. Mechanism testing reveals that this positive effect is mainly achieved by gathering innovative resources and stimulating innovative potential. Further research finds that the effect is more pronounced when the risk of patent litigation is lower, the intensity of cross-regional enlistment is higher, the supply of local talents is greater, and the support of government innovation is weaker. In addition, the system significantly improves the core competitiveness and TFP of enterprises while promoting innovation. This paper not only enriches the study of the micro-governance effect of the “Enlisting and Leading” system, but also provides useful insights and empirical references for the government to stimulate enterprise innovation vitality from a macro-control perspective and address “bottleneck” technological challenges.