Phosphorus (P) fertilizer input influences crop yield, soil P cycling, and phosphate-solubilizing microorganism (PSM) communities, which play a key role in obtaining soil available phosphorus. However, the responses of soil P cycle genes and PSM communities to long-term high-P fertilizer application are less known in the Chinese Loess Plateau. In this study, metagenomics was used to explore the shifts in the abundance and compositions of soil P cycle genes and PSM communities at a long-term (14 years) trial site with four P fertilization rates. Long-term high-P (200 kg P2O5 ha−1 year−1) inputs resulted in a decrease in the abundance of the P-starvation response genes (phoR and phoP), the high-affinity phosphate-specific transporter (pst), the inorganic P-solubilization, and organic P-mineralization genes (gcd, pqq, and phoD). Long-term P inputs increased the abundance of phosphate-solubilizing bacteria but decreased the abundance of phosphate-solubilizing fungi and weakened the relationship of relevant key soil P genes. Soil total P, inorganic P, available P (AP), dissolved organic C contents, and alkaline phosphatase (ALP) activity were significantly related to soil P cycle genes and PSM community structure. In conclusion, the changes in soil P cycle genes and microbial P solubilization capacity under long-term P input conditions were mainly regulated by soil AP content and ALP activity, while long-term high-P inputs increased soil mineral P immobilization by altering the expression of soil P cycle genes and the PSM functional profiles. These consequences provide a new view for the study of soil P cycles in agricultural ecosystems with P inputs.