Background: Taking the construction of ecological civilization as an important core of the overall layout of the “Five in One” and the coordinated promotion of the “Four Comprehensives” strategic layout, combined with the global concept of ecological environment governance, provides a new direction for the reform and innovation of China’s watershed ecological compensation system through diversified governance. Subjects and methods: This article focuses on ecological compensation in river basins, exploring collaborative cooperation models between upstream and downstream of the basin under the dual constraints of “low-carbon” and “water quality”, to achieve a “win-win” situation between the ecological environment of the basin and all parties involved in basin protection. Based on the theory of evolutionary game theory, the indicators of “carbon emissions” and “water quality” are introduced to construct a diversified ecological co-governance compensation strategy model for the watershed. By exploring the optimal strategies among various entities in the upstream and downstream of the watershed. Results: (1) In the initial stage, the optimal strategy for ecological compensation in the watershed among stakeholders cannot achieve a stable balance through their evolution; (2) In the mature stage, based on the regulation of the superior government, interest subjects will choose a mutual supervision strategy to avoid bearing high penalties, to achieve Pareto effectiveness in achieving a stable overall economy of the basin; (3) By paying for high-quality resources from downstream and implementing carbon trading among basin entities, we can promote internal resource digestion, reduce intermediate transaction costs, and deeply promote the overall green and sustainable development of the basin. Through analysis, it has been proven that the conclusion is effective, providing decision support for the diversified co-governance of watershed ecosystems. Based on building an ecological community with a shared future in the watershed, we aim to achieve the construction of a community with a shared future for mankind.