Against the backdrop of the “dual carbon” strategy and high-quality economic development, the coordinated advancement of value chain upgrading and green transformation in manufacturing enterprises is especially critical. However, in reality, enterprises generally face the misalignment of “rapid upgrading but slow greening” or “rapid greening but slow upgrading”, which urgently requires institutional innovation to correct. Taking the chain leader system as the research object, this paper uses micro-level data from A-share manufacturing listed companies from 2009 to 2023 to systematically examine the coupling impact of the chain leader system on corporate value chain upgrading and green transformation development based on a multi-period DID model. The results show that, overall, the chain leader system significantly enhances the coordinated coupling level of value chain upgrading and green transformation in manufacturing enterprises; Mechanism testing reveals that the chain leader system operates through three paths: First, the standard-setting effect reduces deviations from corporate goals, coordinating value chain upgrading and green transformation in direction. Second, the resource allocation effect eases corporate financing constraints, promoting a balance between green investment and R&D upgrading in terms of cost. Third, the long-term incentive improvement effect enhances short-term incentives and corrects inconsistency in the pace of advancement among upstream and downstream enterprises. Further analysis finds that in the short term, the chain leader system mainly plays a role in “quality improving and green supplementing”, with a more significant effect on green transformation. In regions with stronger government intervention, the effect of the chain leader system is more pronounced, indicating that the guiding role of the government in institutional operation is indispensable; in regions with a higher degree of regional integration, the effect of the chain leader system is more pronounced, indicating that spatial integration can amplify the policy effect of the chain leader system. This paper shows that the chain leader system is not only an important institutional innovation to ensure industrial chain stability, but also an effective mechanism for promoting the coordinated development of green manufacturing and value chain upgrading.