The rice-wheat rotation system has been shown to improve agricultural productivity with associated economic benefits. The degree of phosphorus saturation (DPS) refers to saturation of soil sorption sites with phosphorus (P), and reflects the tendency of soil P fixation or release. A current knowledge gap is to investigate how a rice-wheat rotation system affects soil DPS, which is closely related to P loss to the environment. In the present field study, a rice-wheat rotation was established and different fertilization treatments were implemented, and the Anthrosol soils collected from the rice season and the wheat season, were evaluated. Sequential extraction, Langmuir model, and structural equation modeling were used to reveal the proportion of P fractions, P sorption capacity, and the relationships between the degree of P saturation and soil properties, in order to reveal the geochemical mechanisms of P transformation. A higher degree of P saturation is always found in the rice season soils rather than in the wheat season soils, which should be attributed to the lower P retention capacity and the higher presence of P in forms with greater mobility potential in the rice season soils. The reduction of the proportion of residual P fraction coupled with the enhancement of NaHCO3-P/NaOH-P/HCl-P fractions indicated a prevalence of P mobilization due to flooding during the rice planting period. Simultaneously, lower P sorption capacity was also found in the rice season soils. Structural equation modelling was able to confirm that the change of P sorption capacity together with the enhancement proportion labile P in total P, and mobilization of soil residual P combined to affect the degree of P saturation. Management interventions, such as flooding, induced changes from crystalline iron oxides to amorphous iron oxides and this may have enhanced the release of P retained by crystalline iron oxides, which contributed to the mobilization of P in the soils after the rice season. This knowledge can be utilized to avoid P losses to the environment, while still achieving efficient P utilization.