To study the effect of drought stress on morphological characteristics of alfalfa root and bacterial community structure and diversity in alfalfa rhizosphere soil, pot experiment using three root types of alfalfa (rhizomatous rooted Medicago sativa cv.Qingshui, tap rooted M. sativa cv.Longdong, creeping rooted M. varia Martin.cv.Gongnong No.4) as the experimental materials was conducted to set up the drought treatment experiments. The total DNA of the seedling rhizosphere soil was extracted and deep sequencing of V4 region of 16S rRNA gene was performed to characterize the bacterial community structure of drought-treated alfalfa. Compared to the normal condition (CK), the richness index of Chao1 and Ace was the highest under moderate stress, whereas the diversity index of Simpson and Shannon Wiener was not significant under different drought stress. Proteobacteria, Chloroflexi, Bacteroidota, Actinobacteria, and Firmicutes were the special bacteria. The relative abundance of Proteobacteria and Firmicutes dramatically increased, while that of Chloroflexi evidently decreased, whereas that of Bacteroidota and Actinobacteria significantly firstly increased then decreased. The plant height, aboveground and underground biomass, root activity, root volume, and total root length were significantly decreased with increasing of drought concentration, while root shoot ratio increased first and then decreased and reached the most under moderate stress. Under severe stress, the plant height and root activity of M. sativa cv.Qingshui were significantly higher than those of other varieties, while root shoot ratio and underground biomass were significantly lower than those of other varieties. The root length and root tip number of M. sativa cv.Longdong were significantly higher than those of other varieties. There was no significant difference between average root diameter and total root surface area among three root types of alfalfa. Results from this study would present reference to the resistance of plants to drought stress and the improvement of water use of three root types of alfalfa under drought stress.