AbstractSaltwater intrusion in the Changjiang Estuary occurs in winter and dry season, which may affect drinking water supply in Shanghai. An atypical saltwater intrusion event, observed under high river discharge (>20,000 m3/s) in October 2018, coincided with the passage of super typhoon Kong‐rey. The response of the estuarine salt field is reproduced here with a numerical model for analysis with a Eulerian framework. Model results show that saltwater intrusion was mainly due to the landward advection of salt (∼260 t/s), which was driven by the storm surge (∼0.4 m) and landward Ekman transport under typhoon winds. The sheared salt flux (∼145 t/s) significantly contributes to the total landward flux, especially when the surge recedes after the typhoon has passed. Northwesterly winds increased vertical shear and stratification during the event. The maximum saltwater intrusion occurred about a day after the typhoon passage, and the salinity at the freshwater reservoir intake exceeds the local drinking standard of 0.45 psu. A numerical experiment shows that if Kong‐rey had passed during spring tide, the saltwater intrusion would have been weaker due to a stronger northward transport near the coast and a landward transport in the southern channels.