Although ecosystems are valuable, they have been allowed to deteriorate globally in recent decades. However, the spatiotemporal changes in ecosystem-service values (ESVs) and their hotspots in China are not well understood. Here, long-term land-cover data, the spatial analysis method and an econometric analysis model were used to examine these changes. The results indicate that the total terrestrial ESV decreased from US$2398.31 billion in 1990 to US$2347.56 billion in 2010 (converted to 2009 dollar values), which provides strong evidence for the tendency of ecosystems in China to deteriorate over time, albeit slightly. We also found that the changes in ESVs had significant spatial heterogeneity. Our analysis showed that the relationship between ESV and gross domestic product (GDP) is generally negative, but this relationship is not always fixed. The Loess Plateau, Guizhou, Hubei, Henan and Xinjiang continually presented concentrated hotspot areas of ESV changes, whereas coastal regions continually presented concentrated cold-spot areas. Overlap analyses and logistic regressions demonstrate that national ecological programs have clear effects on the improvement of ecosystems but that the effectiveness of different policies varies on spatial and temporal scales. The results of this study will support more effective decision-making around the implementation of ecological conservation policies.