Since the onset of the Three Gorges Project (TGP) in 2003, the sediment load entering the middle Yangtze River (MYR) has been reduced sharply, leading to remarkable channel degradation, which greatly influenced the flood-discharge capacity of this reach. In order to have a better grasp on this situation, there is a need to investigate the variation in flood discharge capacity in this area. Therefore, Chenglingji-Hankou reach (CHR) of the MYR was chosen as a typical reach for this study. Based on the cross-section profiles and hydrologic data surveyed annually from 2003 to 2016, the variations in the relationship between discharge and water-level, the corresponding water-level under the maximum discharge annually, and the characteristics of discharges under certain stages were analyzed at Luoshan and Hankou Stations. The results show that: (ⅰ) water-level under the same discharge decreased in dry season and changed slightly in flood season; water-level under the annual maximum discharge increased compared with that from 1954 to 2002; (ⅱ) the relative discharge under warning water-level at Luoshan and Hankou Stations decreased by 9% and 16%, respectively; (ⅲ) There is no obvious trend in the temporal variation of reach-scale bankfull discharge. The influence factors of the variation in the section-scale flood-discharge capacity were analyzed. It was found that the discharges under the warning water level (at Luoshan and Hankou Stations) were negatively correlated with the bed roughness, which implies that the increase in river resistance is probably one of the main causes of the variation in discharge capacity. Besides, the decrease in relative water-depth ratio and the increase in vegetation coverage on central bars may also show obvious influences on the discharge capacity of the study reach.