In this paper, a three-dimensional hydrodynamic model was coupled to a biological model to simulate the ecological system of the East China Sea. In addition, the sensitive experiments were also used to examine the role of physical forcing (river discharge, wind speed, wind direction) in controlling hypoxia in waters adjacent the Yangtze Estuary. The results showed that the wind field and river discharge have significant impact on the hypoxia off the Yangtze Estuary.