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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. Submerged river deltas are vulnerable to erosion, and this problem may worsen due to the increased frequency and intensity of tropical cyclones (TCs) in the future. However, the impact of TCs on delta erosion is not fully clear. To address this issue, this study deployed four tripods in different parts of the Changjiang River submerged delta during TC Danas (2019). The observed data showed that erosion occurred much faster during the storm than during calm weather. Interestingly, the erosion rate was different at each tripod. A computer model was built to help understand why the erosion rate varied in space. Model results showed that sediment built up in the region where fresh water meets seawater (known as front), since the front can act as a barrier to the seaward movement of sediment brought by the river. In contrast, strong erosion occurred at the offshore edge of the delta. This is caused by diverging ocean currents along widened submerged delta driven by north winds, which carried sediments away from this region. Computer simulations of more storm events confirmed that such erosion can frequently occur at the same location during TCs. This highlights the importance of protecting these areas in the future. Fast erosion near the 30 m isobath of the Changjiang River subaqueous delta (CRSD) was captured by in situ measurement during Cyclone DanasConverging flows near the bottom salinity front led to continuous deposition around the 10 m isobath of the CRSDDiverging isobaths facilitate the erosion of subaqueous delta during downwelling‐favorable storm winds Fast erosion near the 30 m isobath of the Changjiang River subaqueous delta (CRSD) was captured by in situ measurement during Cyclone Danas Converging flows near the bottom salinity front led to continuous deposition around the 10 m isobath of the CRSD Diverging isobaths facilitate the erosion of subaqueous delta during downwelling‐favorable storm winds