Salinity intrusion restricts the exploration and utilization of estuarine freshwater, which is influenced by an important factor, namely the wind. In this study, a numerical model capable of simulating salinity transportation in the Yangtze Estuary is established. Northerly winds prevail in this area in winter, and different wind directions have different impacts on the North Branch and the North Channel. The northeast wind intensifies salinity intrusion in the North Branch, followed by the north wind; however, the northwest wind has a weakening effect on salinity intrusion in the area. The northerly wind aggravates salinity intrusion in the North Channel. The increase in salinity intrusion caused by strong northerly winds has a serious adverse effect on the safety of the Qingcaosha Reservoir. This study provides a basis for the safety of water sources in the Yangtze Estuary.