Choosing the typical typhoon "Nesat", a Modaomen Waterway three-dimensional baroclinic model which was established by the SCHISM model, combined with the Simpson number and salt flux mechanism analysis methods, were applied to study the change process of salinity intrusion dynamic mechanism in Modaomen Waterway during the typhoon transit. The results show that the typhoon caused strong saltwater intrusion in a short time, forming obvious water stratification in the waterway, resulting in a strong longitudinal circulation. It exhibits strain-induced periodic stratification(SPIS)state in the midstream of the waterway during typhoon, and the longitudinal circulation in the waterway is mainly driven by the tidal strain. The salinity distribution showed a double-peak characteristics in this period, which is closely related to the dynamic process of conversion of horizontal flux to land, which caused by the increasing water effect of typhoon "Nesat".