In this study, an East China Sea circulation model was built. Based on this, a small-scale circulation model including the domain of the Yangtze Estuary, Hangzhou Bay, and adjacent water areas was built. With this model, the oceanic current system and coastal current system of the East China Sea, and the flow structure off the Yangtze Estuary were accurately simulated. In order to study the anomalies, typical El Niñ o years were chosen to analyze the response relationship between the nearshore circulation off the Yangtze Estuary and El Niñ o events. The results show that there was a significantly responsive relationship between the nearshore circulation off the Yangtze Estuary and El Niñ o events. In the winter, the circulation at the Yangtze Estuary and adjacent water areas weakened significantly when the El Niñ o phenomenon occurred. The Taiwan warm current was greatly affected, with decreased flow velocity and narrowed flow amplitude, which weakened the impact of the Taiwan warm current on the nearshore circulation off the Yangtze Estuary.