Estuarine areas are vulnerable to the compound effect of flood and storm surges.This paper investigates the response of storm surges at the Yangtze River Estuary to the runoff by analyzing the long-period runoff time-series of Datong Station on the Yangtze River and constructing a three-dimensional (3D) model of storm surges at an estuary with the finite-volume community ocean model (FVCOM).The results suggest the following conclusions：1) The high astronomical (or storm) tide level at the Yangtze River Estuary rises as the runoff increases.They are in a highly linear relationship and can serve as a reference for the forecast of flood and storm surges at estuaries.2) In a given astronomical tide (storm surge) scenario，the water level growth rate only depends on the station’s location.The water level growth rate is higher further in the upstream.3) The storm surge elevation reaches its maximum in the Jiangyin reach，decreases as the runoff increases in the upstream tidal reach from the Jiangyin reach，and undergoes no evident changes in the downstream estuary reach from the Jiangyin reach.