Collaborative eco-environmental governance is an inherent requirement for high-quality regional integration, holding significant implications for advancing China’s ecological civilization strategy and achieving its Dual Carbon goals. This study employs a grounded theory approach, conducting longitudinal coding analysis of transboundary pollution governance data spanning over two decades in the Yangtze River Delta, to construct a theoretical model of quadruple value realization through governance structure restructuring in regional eco-environmental collaborative governance. Findings reveal that as transboundary pollution evolved from single-type to multi-frequency composite patterns, the governance structure transitioned from a unidimensional government-led model to a Party-building-guided, cross-domain, multi-level, and multi-actor framework. This transformation facilitated the integration of institutional, technological, and human capital resources, coupled with closed-loop process optimization, thereby converting environmental, economic, social, and political pressures into four-dimensional value creation. The study emphasizes that governance structure restructuring serves as a critical precondition for resource-process optimization under environmental good governance, with a people-centered responsibility community functioning as the foundational ideology driving such structural evolution. This research extends the application of governance structure theory to cross-domain eco-environmental collaborative governance contexts.