Extreme basin floods can strongly reshape tide-dominated estuaries, but their effects are often conditioned by antecedent channel geometry and human-induced river-bed incision. Here, we investigated the annual-scale morphodynamic response of the North Branch of the Changjiang (Yangtze) Estuary to the 2020 extreme basin flood using hydrological records, bathymetric surveys, surficial sediment samples, and Delft3D scenario experiments. Despite a peak discharge of 83,400 m3 s−1 at Datong, the North Branch showed net shoaling rather than reach-wide erosion over the May 2020–May 2021 survey interval, which encompassed both the 2020 flood and approximately nine months of post-flood adjustment. Mean water depth decreased from 3.35 to 2.91 m, with most channel-volume loss concentrated within the 2–5 m and 5–8 m depth intervals. Erosion was restricted to the bend-apex main channel, the straight middle-channel thalweg, and the mouth-bar area, whereas ebb duration remained longer than flood duration and surficial sediments became coarser and better sorted. Scenario results showed that extreme basin flooding increased the ebb-tide and total diversion ratios by 180.4% and 170.0%, respectively, enhanced the peak ebb current by 37.03% and weakened landward sediment transport. Mid-lower Changjiang channel incision slightly enhanced tidal access under mean-runoff conditions, but model comparisons showed that, under coupled flood and incision conditions, incision attenuated the flood-driven increase in total diversion while further strengthening peak ebb currents. Together, the observations and scenario results support a tide-filtered flood-response mechanism in which extreme flooding promotes local scour and seaward transport, whereas persistent lower-branch tidal import, limited exportable sediment, and reclamation-constrained channel geometry favour internal sediment storage. These findings show that extreme floods in engineered, tide-dominated estuaries may reorganize internal sediment storage rather than produce system-wide erosion.