Aiming at the problem of insufficient coordination of flood control capacity caused by frequent extreme rainstorms and natural water cycle changes in the Yongding River System under the dual stress of climate change and human activities, the “23·7” catastrophic flood in the Yongding River System was used as a case study. The strategy for construction of the hydrological and hydrodynamic flood control model considering the mechanism of runoff generation and confluence and the distribution characteristics of water conservancy projects was adopted, and the universal flood control modeling strategy considering both computational efficiency and accuracy under the framework of digital twin basin was studied. The results show that the flood control model of the Yongding River System can accurately reflect the spatial and temporal variation characteristics of runoff generation and confluence mechanism in different regions during flood process. The model has a high calculation efficiency and accuracy. The 24-d hourly simulation of the whole river system takes 5 min, and the error of the flood peak simulation in the Guanting Shanxia section is within 6%. The maximum inundated area from hydrodynamic simulation in the floodplain is basically consistent with the remote sensing measurement.