Abstract: Economic growth is often accompanied by escalating ecological challenges, making cross-regional collaborative environmental governance a key policy approach. However, practical constraints, such as insufficient governance capacity, high costs, and a lack of accountability mechanisms, hinder regional cooperation in ecological protection. In response, new ecological compensation agreements have emerged. This study examines the effectiveness of the bidirectional compensation strategy and the impacts of various factors on upstream and downstream decision-making, with upstream–downstream cooperation under China’s newly implemented cross-regional ecological compensation agreements as the entry point. Using evolutionary game theory, a cross-regional collaborative governance model is developed, and numerical simulations are conducted to explore the interaction mechanisms between participants and the factors influencing stable strategies. The findings indicate that, first, strategy stability is primarily associated with upstream regions, with compensation amounts, central government incentives, upstream protection costs, and comprehensive benefits exerting varying degrees of influence on the watershed ecological compensation mechanism. Notably, the downstream region exhibits greater sensitivity to compensation amounts than the upstream region, while forgone opportunity costs and comprehensive ecological benefits are critical drivers of upstream environmental governance. Second, the analysis of the central government’s regulatory mechanism within the tripartite evolutionary game underscores the importance of a centrally led governance model in ensuring the long-term ecological integrity of the watershed and promoting fair interregional cooperation. Third, future policy-making should incorporate regional interests to establish more flexible and scientifically grounded ecological compensation mechanisms, fostering coordinated cross-regional governance and achieving a balance between ecological protection and economic growth.