The water-level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) in China has been frequently subjected to drying and rewetting (DRW) since the construction of the Three Gorges Dam. The increased soil labile phosphorus (P) after DRW potentially increases the risk of the release of soil P from the WLFZ to the reservoir water. Our study explored the effects of DRW on the P status of WLFZ soils. In June 2018, surface soil (0–2 cm) samples were taken in the WLFZ at two altitudes of in a tributary (Pengxi River) of the TGR. The labile P and the soil properties were determined in both field-moist and air-dried soils, and the organic P fractions in the bicarbonate extracts were determined through enzymatic hydrolysis. In addition, the contributions of various sources to the increase of soil labile P after DRW were quantified by using the improved organic P fractions tracing method. The results showed that the contents of TP, OP, Olsen-TP, Olsen-IP, Olsen-OP and the proportion of bioavailable P in the field-moist soils at 145 m were significantly lower than those at 165 m. Inorganic P was the main contributor to the increase in P in the bicarbonate extractants following DRW. P_mic, OM and Fe_ox were found to be the main factors influencing the increase in soil labile P after DRW. The organic P fractions, such as diester P, phytate-like P and unknown P, also increased significantly after DRW. The transformation of slowly cycling P contributed 78% and 51% to the increase in Olsen-TP at 145 m and 165 m, respectively, and the death of microorganisms contributed 16% and 18%. The proposed method to quantify the source of increased soil labile P after DRW potentially contributes to reduce the release risk of P from the continent to the receiving aquatic systems.