Phosphatases play important roles in converting organic phosphorus into inorganic phosphorus in soil. However, studies from this perspective on the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir are limited. In this study, phosphatase activity and the forms of phosphorus were analyzed. Soil samples were collected in the river basin of the Penxi River in the WLFZ during a drying period. The correlation between phosphatase activity and phosphorus forms and the impacts of phosphatase activity on the phosphorus forms were analyzed. The results showed that the contents of H2O-Pi, NaHCO3-Pi, and NaOH-Pi in the soils of the WLFZ were higher than those in the soils by the river. In addition, a higher altitude resulted in higher contents of bio-enzymatically hydrolysable phosphorus and NaOH-Po. Furthermore, redundancy analysis (RDA) showed that the contents of organic matter and amorphous Fe and Mn were the main factors affecting soil organic phosphorus forms. The average activities of acid phosphomonoesterase (ACP), alkaline phosphomonoesterase (ALP), phosphodiesterase (PDE) (all in p-NP), and phytase (PAE) (in P) in the soils of the WLFZ were 1.40, 2.60, 0.44, and 11.43 μmol·(g·h)-1, respectively. Moreover, the activities of different phosphatases increased with altitude. Soil plant biomass and microbial biomass were important reasons for the difference in spatial distribution of phosphatase activity in the soil of the WLFZ. Phosphatase activities were significantly positively correlated with the contents of organic phosphorus forms but negatively correlated with the content of bioavailable phosphorus. A higher soil phosphatase activity and a lower content of bioavailable phosphorus were usually detected in soil samples taken at a higher altitude. In the early stage of flooding, phosphatase converted organic phosphorus into inorganic phosphorus at a relatively high rate, and the risk of phosphorus release to the overlying water body was also high. This study contributed to a comprehensive understanding of the geochemical cycle of soil phosphorus in the soil of the WLFZ.