The concentrations of different phosphorus fractions in the soils obtained in the Water-Level-Fluctuation Zone (WLFZ) of the Pengxi River Basin, Three Gorges Reservoir were analyzed. In addition, correlations between these concentrations and different physical-chemical characteristics of the soil samples were also analyzed. The results indicate that the average concentration of total phosphorus (TP) is 599.00 mg/kg. And both the TP and inorganic phosphorus(IP) concentrations gradually decrease with the decrease of altitude. The concentrations of active phosphorous(Ac-P) in the soils of the WLFZ significantly less than those of the riverside at the altitude of 180 m, Ac-P concentrations at the elevation of 155 m, 145 m are close to those of the sediment at the elevation of 140 m but lower than the concentration detected in the samples obtained at the altitude of 165 m. The distribution of Ac-P concentrations at different altitudes indicate that the frequent dry-wet alternations result in the loss of Ac-P in the soils. There is a significent negative correlation between the pH and the TP, IP and Ca-P, meaning the increase in pH result in the decrease in TP, IP and Ca-P, and the organic matter concentration is positively correlated with the organic phosphate concentration, indicating that the input of organic matter affected the concentration of organic phosphate.