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Limited soil and water resources in a sloping karst trough valley have negatively affected the local population and ecosystem health. A deeper understanding of karst ecosystem health and its driving mechanism are important for ecosystem management and restoration. In recent decades, the karst trough valley has been exposed to multiple threats from various natural and anthropogenic factors. Assessment of which is essential to understand the state of the karst ecosystem and to develop a suitable, scientifically proven management strategy. Based on the pressure‐state‐response‐subsystem‐system (PSR‐SS) model, the restored ecosystem health of karst trough valley was assessed from 2000 to 2015 at the grid scale. The principal component analysis (PCA) method was adopted to explore the factors driving ecosystem health change. It is found that from the years of 2000 to 2015, there was an improvement in ecosystem health in karst trough valley ecosystem. Land use analysis maps indicate a slight decrease in woodland and grassland and increase in cropland and urban buildup, and the Land coverage increased from 84.87% to 87.64%. The area of karst rock desertification decreased by 75.3 km2 from 2000 to 2015. The AEH indices of 0.27 (2000), 0.45 (2005), 0.46 (2010) and 0.68 (2015), which indicate moderate warning, pre‐warning, early warning and generally healthy, respectively. The 17 selected driving factors were grouped into two broad categories by PCA, one is national policy, and the other one is natural condition and local activities. National policy was to be found the most important influence on ecosystem health. Our findings emphasize the key role of government in ecosystem health change, which would give directions to the sustainable development of karst trough valley areas. [ABSTRACT FROM AUTHOR]