Inversion of Crop Water Stress Index (CWSI) was conducted based on the evapotranspiration (ET) and potential evapotranspiration (PET) of MODIS. Temporal and spatial variation of drought and its impact on vegetation were analyzed through a variety of statistical methods. The results showed that the annual average drought severity gradually decreased from southwest to northeast, the crops were mainly light and moderate drought, the grassland was mainly medium and heavy drought, and the desert was mainly severe drought. In addition, except coniferous forest and swamp, the drought tendency of other vegetation types was eased. The variation characteristics of annual drought showed a bimodal curve, and the severe drought occurred in 113 to 144 days. The annual variation characteristics of drought severity for each vegetation type were consistent with the change trend of the whole region, showing a bimodal curve. The impact of summer drought on vegetation growth was the strongest, and the stress effect of annual average drought intensity on vegetation growth was mainly dominated by summer drought. For different vegetation types, shrub in spring, crops in summer and autumn were more sensitive to drought. The results could provide theoretical reference for ecological early warning and ecological restoration of plant communities in Inner Mongolia.