In order to explore the differences in the community structures and functions of rhizosphere soil bacteria and root endophytic bacteria of rice with different drought tolerances under drought stress, the sensitive rice E000038 and the drought resistant rice E000039 were taken as the research objects, pot water control method was conducted for drought stress at the seedling stage of rice, and microbial 16S rRNA high-throughput sequencing technology was used to analyze the community and functional diversities of rhizosphere soil bacteria and root endophytic bacteria. The results showed that: 1) Under drought stress, the diversity index α of the endophytic bacterial community of E000038 changed significantly, but α of the rhizosphere soil bacterial community changed insignificantly; But drought stress had no significant effect on α of rhizosphere soil bacterial and root endophytic bacterial communities of E000039. 2) Principal coordinate analysis (PCoA) showed that the bacterial community compositions of E000038 and E000039 rhizosphere soil under drought stress were different from those under normal irrigation; The endophytic bacterial community composition of E000038 roots under drought stress was also significantly different from that under normal irrigation, while the endophytic bacterial community composition of E000039 roots under normal irrigation was similar to that under drought stress. 3) Compared with normal irrigation, the relative abundance of Bacillus in E000038 and E000039 rhizosphere soil bacteria significantly increased under drought stress, the relative abundance of Pseudomonas in E000038 root endophytic bacteria significantly decreased while the relative abundance of Rhodococcus significantly increased; Under normal irrigation and drought stress, the dominant bacteria of E000038 was Pseudomonas with the relative abundance higher than 98.0%. 4) Network analysis revealed that drought stress made the rhizosphere soil bacterial networks of E000038 and E000039 more compact and the structural stability weaker. 5) The functional prediction analysis of endophyte community in roots found that the abundances of enzymes and metabolic pathways with potential drought resistance function were significantly lower in E000038 than E000039 under drought stress. In conclusion, drought stress significantly affects the community diversity of rhizosphere soil bacteria and root endophytic bacteria of sensitive rice E000038, but has no significant effect on the community diversity of rhizosphere soil bacteria and root endophytes of drought resistant rice E000039.