Ecological resilience is an important foundation for conducting regional ecological management. A watershed is a basic unit to conduct ecological management, and in a watershed, the nature-economy-society is a complex composite system. However, what are the links between human activities, management behavior, and the natural environment on a watershed scale? How is the resilience of complex natural-economic-social ecosystems measured? Moreover, in previous studies, little attention was on the watershed scale. Therefore, this study selected the Erhai watershed in China as the study area, constructed an integrated evaluation method of a water-scale complex natural-economic-social system, analyzed the coupling coordination degree of each subsystem, and simulated the changes of ecosystem resilience in the Erhai watershed under different policy scenarios using OWA. The results show that: The resilience of the Erhai Basin from 2005 to 2020 is continuously strong, with the average value increasing from 0.23 to 0.42, but the inter-regional differences increase, and the basin faces the problem of uncoordinated regional development. Fiscal revenues have an important impact on environmental governance behavior, and high fiscal revenues lead to high ecological protection and governance inputs, thus increasing resilience. In the scenario simulation, the ”conservation-first type” has the highest resilience, attaches importance to infrastructure and environmental protection, increases investment in social security and health, and relies on tourism development.