The identification of ecosystem health and its influencing factors is crucial to the sustainable management of ecosystems and ecosystem restoration. Although numerous studies on ecosystem health have been carried out from different perspectives, few studies have systematically investigated the spatiotemporal heterogeneity between ecosystem health and its influencing factors. Considering this gap, the spatial relationships between ecosystem health and its factors concerning climate, socioeconomic, and natural resource endowment at the county level were estimated based on a geographically weighted regression (GWR) model. The spatiotemporal distribution pattern and driving mechanism of ecosystem health were systematically analysed. The results showed the following: (1) the ecosystem health level in Inner Mongolia spatially increases from northwest to southeast, displaying notable global spatial autocorrelation and local spatial aggregation. (2) The factors influencing ecosystem health exhibit significant spatial heterogeneity. Annual average precipitation (AMP) and biodiversity (BI) are positively correlated with ecosystem health, and annual average temperature (AMT) and land use intensity (LUI) are estimated to be negatively correlated with ecosystem health. (3) Annual average precipitation (AMP) significantly improves ecosystem health, whereas annual average temperature (AMT) significantly worsens eco-health in the eastern and northern regions. LUI negatively impacts ecosystem health in western counties (such as Alxa, Ordos, and Baynnur). This study contributes to extending our understanding of ecosystem health depending on spatial scale and can inform decision-makers about how to control various influencing factors to improve the local ecology under local conditions. Finally, this study also proposes some relevant policy suggestions and provides effective ecosystem preservation and management support in Inner Mongolia.