Naturally growing vegetation often suffers from the effects of drought. There exists a vast number of drought indices (DI's) to assess the impact of drought on the growth of crops and naturally occurring vegetation. However, assessing the fitness of these indices for large areas with variable vegetation cover is often problematic because of the absence of adequate spatial information. In this study, we compared six DI's to NDVI (the normalized difference vegetation index), a common indicator of vegetation occurrence and health based on satellite-acquired reflectance data. The study area covers an aridity gradient from forests to deserts along a 2,400-km-long section across the Inner Mongolia Autonomous Region of China. On an annual timescale, standardized precipitation index (SPI) was the most appropriate in assessing drought in steppes and deserts. On a seasonal timescale, the self-calibrated Palmer drought severity index (scPDSI) displayed the greatest sensitivity during the summer, but not during the other seasons. On a monthly timescale, scPDSI demonstrated the greatest sensitivity to the various vegetation zones (i.e., forests, steppes, and deserts) in June and July. Further analysis indicated that summer drought had a lag-effect on vegetation growth, which varied from one to six months according to the specific vegetation cover. The mixed response of DI's to NDVI and the lag-effect in transitional vegetation on annual, seasonal, and monthly timescales were ascribed to differences in DI definition and the dominant plant species within the transitional cover. The current study has the potential to inform the drafting of selection criteria of DI's for the study of drought-related impact on naturally growing vegetation at timescales from month to year.