In recent years, a large-scale afforestation campaign has taken place in Inner Mongolia, China, to control desertification and soil erosion. However, the water consumption associated with large-scale afforestation significantly impacts the water resources in Inner Mongolia, resulting in a substantial ecological risk. This study aimed to evaluate the ecological risk of water resources caused by afforestation in the region. In this study, based on land cover data, Normalized Difference Vegetation Index (NDVI) data, and meteorological data, used trend analysis, water balance equation, and Water resources Security Index (WSI) index to analyze the ecological risks of water resources caused by afforestation in Inner Mongolia from 2000 to 2020. The results show that:(1) The afforestation area in Inner Mongolia was 5.37×104 km2 in 2000-2020; (2) Afforestation in arid and semi-arid areas leads to the reduction of water resources. (3) Afforestation reduces water resources in the study area by 0.76×108m3/year; (4) ~76% of afforestation regions face ecological risks of water resources.