A sharp reduction in sediment load has caused a significant process of channel degradation along the Yichang-Zhicheng Reach after the operation of the Three Gorges Project (TGP), especially in the adjustment of flood discharging capacity. In view of the complicated cross-sectional profiles and the great longitudinal variability in flood discharging capacity, the reach-scale bankfull discharges in the reaches of Yichang and Yidu from 2002 to 2013 were estimated using a combination of geometric average and weighted average method. The effect of channel erosion and deposition on the reach-scale bankfull discharge in each reach was investigated. In addition, empirical relationships were established between the reach-scale bankfull discharge and the previous five-year average fluvial erosion intensity during flood seasons for these two reaches, and it was found that bankful discharge increased with erosion, and decreased with deposition; the correlation between bankful discharge and flow intensity in Yichang was 0.64, whereas in Yidu it was 0.94, indicating that the response of bankfull discharge to the altered flow and sediment regime in the Yidu reach was more remarkable than that in the Yichang reach.