Abstract: The aim of this study is to understand the difference of microbial community in rice root system, the microbial community composition in three niches of endosphere, rhizoplane and rhizosphere was compared. In order to provide a reference for the study of rice root microorganism in the future, this paper explored the relationship between the rice root niche and the variable microbial community. The WGCNA algorithm was used to construct a co-expression network for the microbial community data of the three rice root niches, and the difference networks among the endosphere, rhizoplane and rhizosphere microbial communities were found out. Network was used to compare and analyze the differences of microbial communities among different ecological niches,and co-occurrence network analysis was used to further explore the relationship between different communities.The WGCNA algorithm was used to construct a co-expression network for microbial communities in three niches of rice roots. The results showed that there were differences in the co-expression and interaction networks of microbial community composition among the three niches of rice root endosphere-rhizoplane-rhizosphere. From the further analysis of the difference network among the three niches, we found that: The OTUs in the rhizosphere-rhizoplane difference network were distributed in 18 genera of 6 phylums, and the dominant bacterial phyla was Proteobacteria（72.97%）. The OTUs in the rhizosphere-endosphere difference network distributed in 35 genera of 9 phylums, and the dominant bacterial phyla were Proteobacteria（66.36%）, Actinobacteria（9.09%）, Bacteroides（10.9%）. The OTUs in the rhizosphere-endosphere difference network distributed in 36 genera of 12 phylums, and the dominant bacterial phyla were Proteobacteria（41.41%）, Bacteroides（10.10%）, Firmicutes（12.12%）, Verrucomibia（10.10%）. Three core bacteria genera of Rhodobacter and Novosphingobium, six core bacteria genera of Blvii28 and Dechloromonas, and five core bacteria genera of Cellvibrio and Geobacter, played an important role in the regulation of microorganism co-occurrence network of different populations in rhizosphere-rhizoplane, rhizosphereendosphere and rhizoplane-endosphere, respectively.