By analyzing the response of phoD gene community composition and diversity of farmland soils to different altitudes in Huidong County, Liangshan Mountain, Sichuan Province, We aim to gain an in-depth understanding of the distribution characteristics of phosphorus and the microbial communities involved in phosphorus cycling in farmland soils at different altitudes in the Liangshan Plateau region. This knowledge will provide a scientific basis for establishing a rational fertilizer application system. Soils at different altitudes (1700 m, 1900 m, and 2100 m) in Huidong County, Liangshan, were analyzed for their physicochemical properties, organic phosphorus fractions and contents, and phoD gene communities by chemical analysis and high-throughput sequencing technology. The results showed that pH was positively correlated with altitude. Soil total and effective phosphorus contents were the highest at 2100 m altitude, organic phosphorus (OP), reactive organic phosphorus (LOP), moderately reactive organic phosphorus (MLOP), and moderately stabilized organic phosphorus (MROP) at 1900 m, and inorganic phosphorus content was the highest at 1700 m altitude. For variation of the phoD gene community at different altitudes, Shannon index was the highest at high altitude. Meanwhile, the structure of phoD communities at the three altitudes differed significantly, with Proteobacteria, Actinobacteria and Acidobacteria being the dominant phyla at the three altitudes, while Bradyrhizobium was the main dominant genus at the low altitude 1700 m. Soil pH and total phosphorus (TP) were the key factors driving the composition of soil phoD gene communities at different altitudes. In conclusion, the phoD gene community in farmland soils at different altitudes in the Huidong Plateau region of Liangshan Mountain varied significantly (P<0.05) and was significantly affected by soil pH and total phosphorus (P<0.05). Fertilization measures should be adopted in agricultural production according to local conditions.