Phosphorus (P) is a pollutant of great concern in the Yangtze River Basin. The Xiangjiaba Reservoir and Xiluodu Reservoir on the lower reach of the Jinsha River began to operate in 2012 and 2013, respectively, which greatly changed the concentrations of suspended sediment and characteristics of P form and transport in the reservoirs and the downstream reach from Yibin to Jiangjin of the Yangtze River. The Zhutuo section is representative in the water quality of the Yibin-Jiangjin reach, which can not only reflect the comprehensive effects of the formation of the two reservoirs and changes in the aquatic environment in the Min-Tuo Rivers but also reflect the quality of water flowing into the Three Gorges Reservoir. The runoff, concentrations and fluxes of suspended sediments (SS), and P concentrations and fluxes at Zhutuo section were studied during 2002-2019, and the source of P was apportioned based on the principle of river base flow. The results showed that in the past 18 years, the concentrations and fluxes of total phosphorus (TP) and particulate phosphorus (PP) at Zhutuo section in the wet season were higher than those in the level and dry seasons; the rule of positive correlation between PP and SS concentrations remained unchanged. From 2002 to 2019, the concentrations and fluxes of TP, PP, and dissolved P (DP) generally increased first and then decreased, and the operation of the Xiangjiaba Reservoir was a time node for the trend turning. Compared with that in the period from 2002-2012, the SS concentration and flux decreased by 94% and 77%, TP and PP concentrations decreased by 46% and 70%, and TP and PP fluxes decreased by 58% and 74%, respectively, during 2014-2019. The decline mainly occurred in the wet season, followed by that in the level season. After the formation of the two reservoirs, the relationship between water and sediment and the form of P greatly changed, and the proportion of DP in TP increased significantly, whereas the proportion of PP was the opposite. The TP pool in overlying water in the dry and level seasons shifted from mainly particulate to mainly dissolved. The change in water and sediment conditions was the main driving force for the significant change in P concentration, flux, and form. Before the operation of the Xiangjiaba Reservoir, the Jinsha River was the maximum contributor to the whole and diffuse source part of the TP load at Zhutuo section among the contributing catchment sub-basins; however, the Minjiang River became the largest contributor after the operation. The average TP load at Zhutuo section from 2017-2019 was 3.575×104 t·a-1 (after deducting the natural background value), of which the contribution of diffuse sources and point sources accounted for 68% and 32%, respectively. The Minjiang River represented 49%, 43%, and 62% of the total TP load, diffuse source TP load, and point source TP load at Zhutuo section, respectively. Considering the load contribution and pollution intensity, the key area for P pollution control in the area upstream of the Three Gorges Reservoir was the Min-Tuo River Basin.