This study employed pot experiments that conducted continuous phosphorus deficiency (-P) and phosphorus addition (+P) treatments over five years. In the fifth year, the microbial community structure carrying pqqC genes and inorganic P components in the rhizosphere soil of rice were measured. The results demonstrated that, compared to the +P treatment, the -P treatment significantly increased the Al-P content, reduced the Fe-P content, and simultaneously elevated the copy number of pqqC gene in the soil. The above treatments significantly influenced the composition and structure of pqqC gene-carrying microbial communities. Long-term -P stress increased the Shannon index and Simpson index of pqqC gene-carrying microorganisms in the rice rhizosphere soil, enhancing the relative abundance of Rhizobium, Pseudomonas, Piscinibacter, Rhizobacter and Methylibium. Additionally, pqqC gene-carrying microorganisms showed correlations with various forms of inorganic P in the soil. This study revealed the significant impact of -P stress on the microbial community structure carrying pqqC genes in the rice rhizosphere soil, providing a novel microbiological perspective for improving soil P utilization efficiency.