Subaqueous deltas are facing growing threats of erosion. Tropical cyclones (TCs), which are predicted to affect mid-latitude estuaries more frequently with higher intensity in the future, can play an important role in subaqueous delta geomorphology change. Nevertheless, direct in situ measurement of TC-induced bed elevation change (BEC) was rarely reported before. In this study, four tripods were deployed at different parts of the Changjiang River subaqueous delta (CRSD) to capture BEC during TCs in July 2019. Rapid erosion (20 mm day−1) during TC Danas (2019) was observed by high precision bed elevation measurement, over 10 times faster than that during calm weather conditions. Moreover, the recorded rates of BEC varied substantially among these stations. A coupled three-dimensional wave-current-sediment model was then developed for the CRSD to help understand the spatial variability of observed BEC. The model results showed two striking features of BEC during TC Danas: (a) enhanced sediment accretion near the sharp bottom salinity front offshore of the north channel; (b) marked erosion near the front of CRSD. Further analysis showed that the converging bottom currents in concert with enhanced sediment resuspension during TC Danas led to significant convergence of sediment flux near the bottom salinity front. In addition, the diverging isobaths along the front of the CRSD resulted in the onshore deviation of bottom current and diverging sediment flux under the downwelling-favorable winds of Danas. Many TCs in the CRSD generate similar downwelling-favorable winds and currents, growing TC threats in the future may therefore exacerbate erosion in this region.