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.