The Yangtze Estuary, the largest estuary in China, is under an obvious interaction between runoff and astronomical tide. The research on the interaction is very important for the exploitation and utilization of water resources in this area. A horizontal 2D hydrodynamic numerical model is established and verified in the present study with the modeling range from Datong to the Yangtze Estuary. Based on the comparison of high water levels under the interaction between different runoff and estuarine dynamics, some conclusions are drawn. By revealing the general laws about the relationship between the astronomical tide and flood, the flood level is forecasted to lay a foundation for further research on storm surge in the Yangtze Estuary.