<p>Ecosystem health and human well-being are closely interlinked components of socio-ecological systems, playing a critical role in achieving regional sustainability. We examine the coupling relationship between ecosystem health and human well-being across 228 counties in the middle reaches of the Yellow River Basin—an area facing intense resource and environmental pressure. The main findings are as follows: (1) from 2000 to 2020, ecosystem health in the study area gradually improved, with the average index increasing by 13.61%, mainly driven by enhancements in ecosystem vitality and ecosystem services. However, significant spatial disparities remain, with a pronounced polarization between counties. (2) Over the same period, human well-being increased by 132.29%, but regional inequality also intensified, as indicated by a 31.91% increase in the coefficient of variation. (3) Granger causality tests indicate a bidirectional predictive relationship, significant at the 1% level for one direction and at the 5% level for the other. Impulse response analysis suggests that both systems exhibit self-reinforcing mechanisms, with the magnitude of self-response gradually declining over time. Although ecological improvement and social development may have potential positive mutual influences, these cross-effects were not found to be statistically significant. Spatial analysis shows significant positive spatial autocorrelation within each system, yet a significant negative spatial correlation between them, with dominant cluster types characterized by “high human well-being–low ecosystem health” (distributed in urban agglomerations) and “low human well-being–high ecosystem health” (distributed in mountainous ecological areas) spatial patterns. These findings provide empirical evidence for integrated socio-ecological governance and offer scientific support for coordinated development strategies in large river basin regions.</p>