Understanding the effects of drought on vegetation growth is important for regional ecosystem and water resources management. In this study, the standardized precipitation evapotranspiration index (SPEI) and normalized difference vegetation index (NDVI) were used to analyze the relationship between drought activity and vegetation dynamics at different time scales in the Kaidu River basin from 2000 to 2018. The results showed that (1) during this period, annual, summer and autumn SPEI showed an increasing trend, while spring SPEI showed a decreasing trend. Annual, spring, summer and autumn NDVI showed an increasing trend. (2) In the Kaidu River basin, the percentage of areas with an increasing trend of SPEI in annual, spring, summer and autumn were 85.98%, 41.93%, 65.86% and 98.73%, respectively. However, none of them reached the 0.05 significant level. The trend of NDVI is more obvious than that of SPEI. The proportion of regions with significant increasing trend of NDVI in annual, spring, summer and autumn were 24.10%, 23.63%, 23.06% and 19.15%, respectively. (3) Vegetation growth was positively correlated with drought in most areas of the Kaidu River basin. The percentage of regions with positive correlation between SPEI and NDVI in annual, spring, summer and autumn were 24.10%, 23.63%, 23.06% and 19.15%, respectively. However, the correlation coefficients between SPEI and NDVI were significantly different for different seasons and different vegetation types. (4) The residual analysis revealed that 33.20% of the vegetation in the Kaidu River basin was degraded by human activities and 66.80% was improved by human activities. Similarly, the climatic conditions of the region promote the growth of most vegetation. This study provides a useful reference for vegetation construction and water resources management in inland river basins in arid regions.