Prefabricated buildings in water conservancy projects have significant potential for promoting sustainable development, but their complex supply chain structure and synergistic benefits have not yet been fully realized. Existing research mainly focuses on measuring benefit outcomes, lacking a systematic analysis of the driving mechanisms of synergistic benefits. This paper, based on the resource-based perspective and institutional theory, constructs a supply chain synergistic benefit driving model from the perspectives of single effects and multi-factor configurations. Using 648 sample data points, it conducts an empirical study employing structural equation modeling (SEM) and fuzzy set qualitative comparative analysis (fsQCA). The results show that resource capacity, economic incentives, 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, economic-technical, cultural-technical, and total factor equilibrium. This research reveals the multi-factor driving mechanisms of synergistic benefits in the supply chain of prefabricated buildings in water conservancy projects, providing theoretical and practical references for project synergistic optimization and high-quality development of the industry.