The changes in total phosphorus (TP) concentration and form in the Three Gorges Reservoir (TGR) from 1998 to 2019 were studied, and P fluxes were calculated. The entire research period was divided into three stages: 1998–2002 (stage I, before the operation of the TGR), 2003–2012 (stage II, as a transitional period), and 2013–2019 (stage III, after the TGR achieved the normal water level of 175 m and Xiangjiaba Reservoir began to operate). Comparative analysis was mainly on Stages I and III. The results show that the concentrations of suspended sediment (SS) in the TGR decreased to a very low level (average 42 mg/L during 2013–2019 period and 96 mg/L in wet season). From 1998 to 2019, the inflow and outflow of sediment amount showed a downward trend. A huge amount of sediment was retained at the bottom of the reservoir during 2003–2012 (average 154.6 million t/a), while in 2013–2019, the amount of sediment deposition significantly decreased and the sedimentation amount was only 37% of that in 2003–2012. Year 2013 marked a turning point in the trend of phosphorus pollution in TGR from increasing to decreasing. Afterwards, concentrations of TP and DP (dissolved phosphorus) showed a significant downward trend. The form of phosphorus in TGR changed from mainly granular to dissolved, and the percentage of DP in TP in the perennial backwater area increased from 39% before TGR formation to 69% during 2017–2019. 2004–2012 was a period with high deposition for TP when the amount of TP entering the reservoir was large and fluctuated vastly between years, and approximately 60% of phosphorus was trapped (82220 t/a). From 2013 to 2019, there occurred significantly decrease in the TP amount entering the reservoir in accompany with diminishing interannual fluctuation, tending to a balance between input and output of P. Fluxes of TP, DP, and PP (particulate phosphorus) all show a pattern of wet season>even season>dry season. The main driving forces for changes in TP concentration, flux, and form are the reduction in SS concentration and phosphorus pollution level.