In order to explore the differences in rhizosphere soil and root endophytic bacterial community structure and function of rice with different drought tolerance under drought stress, this study took sensitive rice E000038 and drought resistant rice E000039 as the research object, and adopted pot water control method to implement drought stress at seedling stage, and adopted microbial 16 S RNA high-throughput sequencing technology. The communities and functional diversity of rhizosphere soil bacteria and root endophytic bacteria were analyzed. The results showed that leaf drying and curling appeared in E000038 after drought stress, but the growth of E000039 was not affected. Drought stress significantly affected the α diversity index of the root endophytic bacterial community of E000038, but the α diversity index of the rhizosphere soil bacterial community did not change significantly, and the diversity of the rhizosphere soil bacterial community and the root endophytic bacterial community of E000039 had no significant effect. The results of bacterial community structure analysis showed that after E000038 and E000039 drought stress, the rhizosphere soil bacteria Bacillus increased significantly, which may be involved in rice drought stress response. Before drought stress, the dominant bacterial groups of E000038 and E000039 endophytic bacteria were all Pseudomonas, and the relative abundance was higher than 98.0%. After drought stress, the relative abundance of Pseudomonas in E000038 decreased significantly, but the relative abundance in E000039 did not change significantly. The analysis of root endophyte community function showed that the abundance of potential drought resistant enzymes decreased significantly after E000038 drought stress compared with E000039. Compared with rhizosphere soil bacteria, the community composition and potential functions of endophytic root bacteria were more sensitive to drought response. The results of this study provided a theoretical basis for improving rice drought resistance by using microbial resources effectively.