To elucidate the differences in inter-root bacterial communities of Aquilaria sinensis, and to explore the correlation with soil physicochemical properties, we used the high-throughput sequencing technology and bioinformatics-related tools to analyze the composition and multi-characteristics of the inter-root soil bacterial community of A. sinensis. In three cultivation sites in Hainan province (Wenshan village, Haikou city, Dongguang farm, Lingao, and Baolun farm, Ledong), and combined with redundancy analysis to correlate the inter-root soil physicochemical proper-ties with the bacterial community. The results showed that a total of 7 944 402 sequences belonging to 51 phyla,151 orders, 380 families, 637 families, 1296 genera and 2649 species were obtained among the sites; the variability of bacterial community and diversity of A. sinensis in the sample sites was not significant, and there were significant differences among the sample sites. The richness and diversity of inter-root soil bacteria in the sites were as follows: LDJX>LDWJ>LGWJ>LGJX>WSWJ>WSJX. In terms of community structure, the Ledong sample site differed significantly from the Wenshan and Lingao sample sites in terms of community structure.at the phylum level, the dominant bacterial phyla in Ledong were Planctomycetota, Chloroflexi, and Verrucomicrobiota; the dominant populations in Wenshan and Lingao were Firmicutes, Bacteroidota, and Proteobacteria. At the genus level, the dominant genera in Wenshan and Lingao were Bacteroides, uncultured_bacterium_f Muribaculaceae, and Faecalibacterium; the dominant genera in Ledong were the unidentified genus (g_uncultured_f__Gemmataceae) genus, Candidatus_Udaeobacter, and Bacteroides. The RDA analysis revealed that the inter-rhizosphere soil bacterial community of A. sinensis was affected by soil physicochemical factors with some differences among different sites. Total phosphorus was significantly and negatively correlated with bacterial population differences and diversity, and pH was significantly and positively correlated with bacterial population differences and diversity. The results are valuable for studying the interactions of inter-root microorganisms of A. sinensis, and have certain guiding significance for the development of Hainan incense industry.