The objective of this study was to investigate the endophytic bacterial communities in the seeds of three rice (“Shen 08S”, “He 620S” and “16A007”) in maturity stage. Experimental results showed that the parental seeds of hybrid rice had diversity of the bacterial community structure at maturity stage. The endophytic bacterial communities in “Shen 08S” included 40 OTUs, they were belonged to Firmicutes,Proteobacteria,Actinobacteria and Bacteroidetes, among them, the abundance of the first dominant bacterium Rhizobium was 15.83%, the second and third dominant bacterium was Bacillus, the third dominant bacterium was Sphingomonas and Curtobacterium; The endophytic bacterial communities in “He 620S” included 20 OTUs, they were belonged to Firmicutes,Proteobacteria and Actinobacteria, the abundance of the first dominant bacterium Curtobacterium was 25.33%,the second and third dominant bacterium was Microbacterium and Pantoea, respectively; the endophytic bacterial communities in “16A007” included 24 OTUs, belong to Firmicutes,Proteobacteria and Actinobacteria, the abudance of the first dominant bacterium Pantoea was 35.00%, the second and third dominant bacterium was Micrococcus and Pseudomonas, respectively.From this study, we found that the endophytic bacteria species in the seeds changed with seed maturation, and the seeds in maturity stage were richer in endophytes resources, which can lay the foundation for the development of new microbial inoculants, and the endophytic bacterial community structure has certain relevance in the seeds of hybrid rice which are genetically related.