The floods occurred in the Three-Gorge Reach of the Yangtze River due to rainstorms have most important influence for the safety and operation of the Three-Gorge Reservoir. Toward reducing the uncertainty of flood forecasting as much as possible, a distributed hydrological model based on characteristics of catchment geomorphology was developed, which could describe the spatial variability of topography, land use, soil properties as well as its hydrological responding to rainfall. In this paper, model calibration and validation was done by means of the hourly rainfall measured at raingauges as model input, and discharge data observed at hydrological stations as the comparison of model output. The results show that most of flood processes can be simulated well and the dominated uncertainty to reduce the accuracy of flood modeling is inadequate information of rainfall input.