The Digital Elevation Drainage Network Model is used for the determination of raster flow vectors, the delineation of subcatchments, and the extraction of river network from the digital elevation model data. On the basis of two ways of spatial discretization: grid and subcatchment, three methods are applied to processing precipitation data as the input of hydrological model, so as to analyze the effect of spatial precipitation heterogeneity on runoff process. The first is the conventional subcatchment method by taking directly rain -gauge data measured within the subcatchment as the input of the subcatchment. The second is modified subcatchment method by interpolating rain- gauge data to each grid, then averaging rain values over all grids within a subcatchment as the input of the subcatchment. The third is one-grid by one-grid method by taking rain value interpolated to a grid element as the input of that element. Those three methods are utilized for the simulation of daily runoff and flood discharge, respectively. A case study in the Baohe catchment shows that three methods make little difference in the computation of daily discharge, while the one-grid by one-grid method performs better than the conventional subcatchment and the modified subcatchment methods in flood discharge modeling in terms of model efficiency coefficient. The conclusion can be drawn that the more sufficiently the spatial rain heterogeneity is taken into consideration, the higher the accuracy of flood modeling is.