Abstract: Many tributaries exist in the Three Gorges Reservoir area, when the reservoir has been constructed and stored water, the original natural river channels and they nearby slope were submerged, forming a relatively wide artificial lake, resulting in big change of rainfall-runoff. In order to study the influence of water level change on the rainfall and runoff, MIKE model and statistical nonlinear regression model were used to simulate the flood process in the reservoir area. The results show that both water level change of reservoir construction and different water level operation are conducive to rainfall-runoff generation, the rise of reservoir water level has a certain gain effect on flood peak discharge, accelerating the process of runoff generation and concentration. The water level have a certain impact on the hydrological and hydraulic, but this impact is limited, the natural conditions still play a decisive role in the flood. This research results can provide some technical suggestions for the prediction and operation of Three Gorges Reservoir.