The development of institutional systems is the cornerstone of ecological governance and an important dimension for measuring Chinese modernization. From the perspective of the synergistic empowerment, this paper constructs a three-dimensional framework of institutional synergy, co-existence of subjects, and efficiency transformation, breaks traditional governance boundaries, and forms an interaction mechanism featuring clearly defined responsibilities and high-efficiency collaboration among multiple entities, exploring ways to enhance the effectiveness of ecological governance and sustainable development capabilities through institutional innovation and collaborative governance by multiple entities. This paper finds that significant achievements have been made in the construction of ecological civilization in China. However, issues, such as insufficient embeddedness of the governance system, decreasing policy effectiveness, imbalance of main bodies, difficulties in institutional collaboration, inadequate capability, and lack of cross-regional systems, still constrain the deepening of ecological governance reforms. There is an urgent need to promote the transition of the governance system from “top-down promotion” to “synergistic empowerment” through institutional innovation. This transition breaks through the limitations of single-entity efforts, providing a new analytical perspective for resolving deep-seated contradictions in ecological governance. It promotes the dynamic adaptation of “effective institutions” and “active government” through institutional empowerment, strengthens the organic linkage between “good institutions” and “good governance” through collaborative governance of main bodies, and realizes the resilient construction from “mechanical control” to “organic synergy” through paradigm leapfrogging. To achieve synergistic empowerment in the ecological civilization system, it is necessary to establish the concept of modern ecological governance, activate institutional potential, optimize institutional connections, and ensure strong implementation. Specific paths include reshaping the concept to anchor the direction of modern ecological governance, leveraging supply-side reforms to activate the productivity of basic institutions, connecting institutions to enhance the adaptability of coordinated institutions, and ensuring strong implementation to unleash the overall effectiveness of fundamental institutions, aiming to effectively improve the growth capacity and operational efficiency of institutional synergy and continuously meet the people’s needs for a beautiful ecological environment.