[Objective] Our study aims to understand the microbial diversity of endophytic bacterial community of different rice tissues.[Methods] We adopted high-throughput sequencing technology to study the microbial community structure and composition of bacterial endophytes in rice plant. We extracted DNA of the microbial community of bacterial endophytes in the rice var. No. 43 of Ningjing. The bacterial 16S rRNA gene hypervariable region V5-V7 was detected by high-through sequencing technologies.[Results] In total 610 OTUs were obtained from leaf bacterial endophytes, 411 OTUs from rice stem, 174 OTUs from rice root. Based on the results of species classification, leaf endophytic bacteria were represented by 22 phyla that mainly comprised 40 classes, 103 orders, 198 families, and 399 genera. Among them, the predominant genera were Rhodococcus and Lactobacillus, and their relative abundances were 21.00% and 9.19%, respectively. Stem endophytic bacteria were represented by 19 phyla that mainly comprised 31 classes, 85 orders, 169 families, and 306 genera. Among them, the predominant genera were Rhodococcus and Ralstonia, and their relative abundances were 19.25% and 13.52%, respectively. Root endophytic bacteria were represented by 9 phyla that mainly comprised 19 classes, 44 orders, 82 families, and 140 genera. Among them, the predominant genera were Enterobacter and Escherichia, and their relative abundances were 81.13% and 10.89%, respectively. Seventy-eight of the OTUs were represented in all the rice endophytic samples. Actinobacteria were strongly associated with other bacteria. The higher species abundance of root bacterial endophytic community could regulate various metabolic networks compared to the stem and leaf.[Conclusion] The diversity of bacterial endophytic community associated to rice plants has important ecological significance.