An incubation experiment was conducted using soils taken from tobacco-planting filed in Liupanshui City of Guizhou to explore the effects of green manure incorporation on soil phosphorus availability and its underlying microbial mechanism. Three types of green manure, vetch, rape and ryegrass were selected as exogenous organic materials and incorporated into tested soils. After 30 days of incubation, soil samples were taken to analyze organic acid content, microbial community function and phosphatase activity. The results showed significant increases in available phosphorus content, average well color development (AWCD) and phosphatase activity under green manure treatments compared with the control treatment, among which vetch had the highest enhancements. In addition, the total amount of organic acids, especially citric acid content was significantly higher under vetch treatment than under other treatments. Random forest analysis and structural equation model results indicated that AWCD, phosphatase activity and organic acids concentrations were the key factors regulating available phosphorus content, among these factors AWCD showed direct effect, and moreover, AWCD also indirectly affected available phosphorus content via influencing soil phosphatase activity and organic acids concentrations of which promoting phosphatase activity by microbial activity was the primary pathway to improve soil phosphorus availability.