Microbial community and functional genes associated with phosphorus (P) cycling are intrinsic to soil P transformation. Yet, how the P fertilization rates affect the interactions of the microbial community and functional genes of P profiles is urgently needed to improve fertilizer P utilization efficiency. To address this, we conducted a long-term field experiment on purple acid soil in southwestern China using five mineral P fertilization rates. We analyzed the amplicon and metagenomic sequencing data to investigate the impact of P application rates on the bacterial and fungal communities as well as P cycling genes. Our results indicate that the community structure of both microbes and functional genes was significantly affected by P fertilization. Compared to other P levels, P application at 33 kg P ha−1 significantly increased the average degree and cohesion in the bacteria-fungi network, while the interactions between P cycling genes and microbes were also complex. Meanwhile, P application up to 16 kg P ha−1 increased the abundance of dominant functional genes (gcd and phoD), which were negatively correlated with Po and Pi. Nocardioides, Candidatus Solibacter, and Gaiella were the dominant taxon that induced the P cycling. The partial least squares path model (PLS-PM) revealed that SOM and pH were the main factors influencing AP by affecting the diversity and cohesion of the bacteria-fungi community, as well as gene abundance of P cycling genes under long-term gradient P fertilization. Overall, these results highlight the potential of moderate P fertilization to promote the stability of the microbiology and P transformation in acid soil.