Phosphorus (P) is a pollutant of great concern in the Yangtze River basin, which has an important impact on the water ecology of the Yangtze River basin. The P flux and form at the Three Gorges Reservoir (TGR) outlet section during 1998-2019 were studied, and the whole period was divided into three stages: 1998-2002 (stage Ⅰ, pre-TGR period), 2003-2013 (stage Ⅱ, as interim period), and 2014-2019 (stage Ⅲ, after TGR achieved 175 m normal water level and completion of Xiangjiaba Reservoir and Xiluodu Reservoir), and Ⅰ and Ⅲ as key periods in comparison. The results show that the average annual total phosphorus (TP) flux in stage Ⅲ was 5.67×10⁴ t/a, 38.0% less than that in stage Ⅰ. Wherein, dissolved phosphorus (DP) flux and particulate phosphorus (PP) flux were 4.02×10⁴ t/a and 1.67×10⁴ t/a in stage Ⅲ, with an increase of 60.0% and a decrease of 74.9% comparing to stage Ⅰ, respectively. The main form of P has changed from particulate to dissolved. In 1998-2002, the DP flux accounted for 27.5% in TP flux, but rose to 70.9% in 2014-2019. Accordingly, the percentage of PP flux decreased from 72.5% to 29.1%. Seasonality of TP, DP and PP flux are shown as wet season>even season>dry season. In the past two decades, the relationship between runoff (Q) and suspended sediment (SS) has changed greatly, and the positive correlation between them has decreased significantly, the slope of correlation equation decreased from 1.44 to 0.10, and R² from 0.83 to 0.57. The rule that the percentage of monthly DP flux decreases with increasing SS remains unchanged, and the empirical model was established as λ_DF=1.2883-0.3688×lgSS (mg/L) based on data during 2014-2019. The changes of P flux and form characteristics were mainly attributed to sediment trapping of three reservoirs and soil and water conservation in the basin. Attention should be paid to the ecological effects resulted from the increase of bioavailable P concentration and the enhancement of light energy absorption.