Phosphorus in agro-ecosystems has attracted much attention due to its impact on the nutrient supply of plants and the risk of loss of non-point source pollution. This study investigated the fraction distribution and release of phosphorus from soil aggregates structure under different land uses (rice, maize and soybean). The soil aggregates were characterized as large macro-aggregates (L-mac, >1 mm), small macro-aggregates (S-mac, 0.25–1 mm), micro-aggregates (MIC, 0.053–0.25 mm) and silt clay (SC, <0.053 mm) with the wet-sieving method. A sequential chemical extraction scheme was used to separate phosphorus into labile inorganic phosphorus (L-Pi), labile organic phosphorus (L-Po), moderately labile organic phosphorus (Ml-Po), iron-aluminum bound phosphorus (Fe.Al-P), calcium-magnesium bound phosphorus (Ca.Mg-P), humic phosphorus (Hu-P) and residual phosphorus (Re-P). Experimental results indicated that soil aggregates were mainly S-mac and MIC, followed by L-mac and SC, and they accounted for 52.16%, 25.20%, 14.23% and 8.49% in rice fields, 44.21%, 34.61%, 12.88% and 8.30% in maize fields, and 28.87%, 47.63%, 3.52% and 19.99% in soybean fields, respectively. Total nitrogen (TN), soil organic matter (SOM), Fe and Mn in soil aggregate fractions decreased with the reduction in soil aggregate grain-sizes. For phosphorus fractions (P-fractions), Fe.Al-P and Re-P tended to condense in L-mac and S-mac. MIC and SC were the primary carriers of Ca.Mg-P. Adsorption isotherm simulation results demonstrated that L-mac and S-mac have a strong capacity to retain phosphorus. In rice fields, phosphorus bioavailability and utilization rate were high. However, the P-fractions there were easily changed under aerobic-anaerobic conditions. Therefore, the risk of phosphorus loss during drainage should be given considerable attention.