Matching the location of the input data, such as the radar rain rate and the topographical information data, is very important in the rainfall-runoff process. If the radar rain rate and the topographical information data have different coordinate systems, the locations of the two types of data will not match. Moreover, the wind effect hinders the matching of the locations of the radar rain rate and the topographical information data. In this study, the runoff uncertainty caused by the mismatch between the radar rain rate and the topographical information data with respect to the horizontal drift distance was quantified. As a result, when the horizontal drift distance of the water drop observed at altitude of 1.5 km was 1 km, the location mismatch between the radar rain rate and the topographical information data produced a total volume error of 3.88±6.13% in the 95% confidence interval, a peak flow error of 3.14±6.33%, and a peak time error of 0.34±1.22%. When the horizontal drift distance increased to 4 km, the error of total volume, peak flow, and peak time increased to 7.52±10.27%, 5.96±10.90%, 3.27±23.48%, respectively.