Long-term wetland reclamation has significantly altered soil phosphorus (P) fractions and microbially mediated P-cycling processes in agricultural ecosystems. In this study, we investigated the evolutionary trends and correlations among soil physicochemical properties, P fractions, and microbial P-cycling genes in dryland and paddy soils across a 3000-year soil chronosequence in the Yangtze River floodplain. This was achieved using an integrated approach combining metagenomic sequencing, the sequential extraction (SEDEX) method, and a "spacefor-time" substitution strategy. During the early reclamation duration (60-280 years), P fractions, including exchangeable P (ExP), iron-bound P (FeP), authigenic P (CaP), detrital apatite P (DeP), and organic P (OP), increased significantly due to natural weathering and anthropogenic inputs but declined after 2000 years of reclamation. Results showed that paddy soils generally exhibited higher levels of total P, ExP, and OP than dryland soils. The richness and diversity of microorganisms involved in P-cycling were relatively high in the early stages but decreased to their lowest levels by 3000 years. Correlations among microbial genes, soil physicochemical properties, and P fractions were stronger in dryland soils. Path modeling further revealed that reclamation duration influenced the abundance of microbial P-cycling genes indirectly through soil properties and P fractions. This research enhances our understanding of P cycling in dryland and paddy soils under long-term wetland reclamation and provides a scientific foundation for promoting regional sustainability and efficient P resource management.