Rapid industrialization and urbanization have accelerated land-use changes in mountainous areas, with dramatic impacts on ecosystem health. In particular, the Qinling-Daba Mountains, as China’s central water tower, ecological green lung, and biological gene bank, have rich resource endowments and extremely high ecological value and are an important protective wall to China’s ecological security. Therefore, understanding the level of ecosystem health and its drivers in the research area contributes to the conservation and restoration of the mountain ecosystem. Based on remote sensing image data and land-use data from 2000 to 2020, we explored the spatial characteristics of ecosystem health, and supplemented with socio-economic data to explore its driving factors. The results show that (1) the ecosystem health in the study area has been continuously improved during the study period, and the regional differences in ecological organization are the most prominent; (2) the level of ecosystem health in the Qinling-Daba Mountains has been spatially improved from the peripheral areas to the central area, showing significant spatial autocorrelation and local spatial aggregation; (3) the ecosystem health is influenced by a combination of natural and anthropogenic factors, among which the negative effect of GRDP is mainly concentrated in the eastern region, the negative effect of the proportion of built-up land gradually spreads to the western region, and the positive effect of the proportion of forest land has a large scale. This study contributes to a better understanding of ecosystem health in mountainous counties in China and provides useful information for policymakers to formulate ecological and environmental management policies.