Prefabricated buildings in water conservancy projects have significant potential in promoting sustainable development, but their complex supply chain structure and synergistic benefits have not yet been fully realized. Existing research focuses primarily on measuring benefit outcomes, lacking a systematic analysis of the driving mechanisms of synergistic benefits. Based on the resource-based perspective and institutional theory, this study constructs a supply chain synergistic benefit driving model from the perspectives of single effects and multi-configuration. Using 648 sample data points, an empirical study is conducted using structural equation modeling (SEM) and fuzzy set qualitative comparative analysis (fsQCA). The results show that resource capacity, financial capacity, technological support, policy support, governance mechanisms, and cooperative culture all significantly promote synergistic benefits, with resource capacity and governance mechanisms playing the most prominent roles. Synergistic benefits arise from the combined effects of multiple factors, forming five typical paths: resource-driven, policy-governance, financial-technical, culture-technology, and total factor equilibrium. Therefore, improving synergistic benefits requires differentiated configuration management. Enterprises should choose appropriate paths based on their own conditions, promote the deep integration of cooperative culture and technological support, strengthen the synergistic linkage between internal resource endowments and the external institutional environment, and maximize the overall value of the supply chain.