Abstract. The phenomenon of low dissolved oxygen (known as hypoxia) in coastal ocean system is closely related to a combination of anthropogenic and natural factors. Marine hypoxic occurs in the Yangtze Estuary, China with high frequency and long persistence. It’s known that it related primarily to organic and nutrient enrichment influenced by river discharges and physical factors, such as water mixing. In this paper, a three-dimensional hydrodynamic model was coupled to a biological model to simulate and analyze the ecological system of the East China Sea. By comparing with the observation data, the model results can reasonably capture the physical and biochemical dynamics of the Yangtze Estuary. 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 to the Yangtze Estuary. The results showed that the wind field and river discharge have significant impact on the hypoxia off the Yangtze Estuary. The seasonal cycle of hypoxia was relatively insensitive to synoptic variability in the river discharge, but integrated hypoxic areas were sensitive to the whole magnitude of river discharge. Increasing the river discharge was shown to increase hypoxic areas, while decreasing the river discharge was tended to decrease hypoxic areas. And the variations of wind speed and direction had great impact on the seasonal variability of hypoxia and the integrated hypoxic areas.