Abstract: In order to explore the microbial regulation mechanism of PGPR on soil phosphorus cycle, tobacco planting fields treated with bacterial, fungal and actinomycete PGPR inoculum respectively in Huili City, Liangshan Prefecture, the cultivated soil in the mature period of flue-cured tobacco was collected to conduct. Chemical analysis and high-throughput sequencing, and soil physical and chemical properties, phosphatase activity, and the composition and diversity of bacterial community containing phoD gene were analyzed. The results showed that the application of three PGPR agents could significantly increase the content of soil organic carbon, total nitrogen, available phosphorus and available potassium, among which the actinomycete PGPR agent could significantly increase the phosphatase activity of soil; PGPR could also improve the diversity of phoD community in tobacco planting soil. The dominant bacteria at the phylum level were Actinobacteria, Proteobactera and Cyanobacteria, and the dominant bacteria at the genus level were Streptomyces, Amycolatopsis and Bradyrhizobium; Redundancy analysis showed that available potassium, pH, available phosphorus and other environmental factors were the main factors affecting the community structure of bacteria containing phoD gene in tobacco planting soil. To sum up, PGPR can significantly improve the nutrient status of tobacco planting soil, increase soil phosphatase activity, and change the structure of phoD gene community in the cultivated layer of flue-cured tobacco.