Ammonia nitrogen (NH4+-N) and total phosphorus (TP) were the major control pollutants in the Yangtze River Basin. Based on measured data from 2003 to 2020, the temporal and spatial variations in concentrations and fluxes of NH4+-N and TP in the Jianli to Hankou (JL-HK) reach of the Middle Yangtze River were studied, and the impacts of flow-sediment factors, tributary inflows, and others on variations in NH4+-N and TP fluxes were discussed. The results showed that: ① In recent years, NH4+-N and TP concentrations in the mainstream have declined significantly, with annual NH4+-N and TP concentrations at each monitoring station in 2020 averagely decreasing by 41% and 34% compared to those in 2003, respectively. Spatially, NH4+-N and TP concentrations decreased and then increased along the mainstream. NH4+-N and TP concentrations of tributary inflows, which include the Dongting Lake and Han River, were generally lower than that of the mainstream. The multi-year average values of NH4+-N and TP concentrations were both averaged at 0.12 mg·L-1 in the mainstream and were averaged at 0.11 mg·L-1 and 0.09 mg·L-1 in the tributary inflows. ② The flux differences between the upper and lower sections net of tributary confluences showed that NH4+-N and TP fluxes were lost in the Jianli to Luoshan (JL-LS) sub-reach and increased in the Luoshan to Hankou (LS-HK) sub-reach in most years. NH4+-N and TP fluxes decreased in the JL-LS sub-reach, which was related to the lower NH4+-N and TP concentrations in lateral inflows, such as Dongting Lake, and thus lowered the NH4+-N and TP concentrations in the mainstream. The LS-HK sub-reach showed the opposite trends, and the water and sediment loads increased in this sub-reach. Across the whole JL-HK reach, TP flux as well as water and sediment loads were recharged along the reach, whereas NH4+-N flux was reduced greatly, which could be attributed to the pollution abatement conducted in the Yangtze River Basin, which mainly focused on NH4+-N. ③ The correlation analysis results showed that NH4+-N fluxes had the strongest correlation with NH4+-N concentrations but not significantly correlated with discharges and sediment transport rates, indicating that NH4+-N was mainly controlled by point source pollution in the study reach. TP fluxes had higher correlations with discharges and sediment transport rates in high flow level periods, and the correlations between TP fluxes and TP concentrations were better in low flow level periods, reflecting that point source pollution contributed more to TP in dry seasons compared to flood seasons.