Ecosystem restoration is an urgent and vital measure to restore degraded land in ecologically fragile regions. The terrestrial carbon sequestration capacity is important to indicate the effectiveness of ecosystem restoration, which has attracted the interest of many researchers. Ecologically fragile regions cover a large area in China, but few studies have focused on the carbon benefit of ecological restoration in these regions. In this study, we investigated the spatial and temporal changes in the carbon benefit, indicated by net primary productivity (NPP), in ecologically fragile regions in China. We evaluated the contributions of ecological restoration and climate change to terrestrial ecosystem carbon sink changes. The results showed that the ecological restoration projects significantly improved the carbon sequestration capacity in most of the ecologically fragile regions. From 2001–2017, the annual NPP of the entire study region was 460.1 ± 5.4 Tg C yr−1, and more than 70 % of the ecologically fragile region experiencing a significant (p < 0.05) increase. The effect of ecological restoration projects significantly intensified and was the main driver of the NPP growth in 87 % of the study region. The land use and land cover (LULC) change pattern indicates that the restoration project-induced conversion of agricultural land contributed to nearly 10 % of the total carbon sequestration after 2010. However, some extreme climatic conditions weakened the effectiveness of ecological restoration projects, highlighting the need for stricter management. Finally, this study identified the key area for effective ecological restoration in ecologically fragile regions in China.