<p>The spatial scale mismatch between runoff generation and runoff routing is an acceptable compromise but a common issue in hydrological modeling. Moreover, there is hardly any report on whether a unit hydrograph (UH) consistent with the spatial scale of runoff generation can be computed. This study aimed to investigate the impact of spatial heterogeneity in runoff generation on a UH for flood prediction. To this end, a novel GIS-based dynamic time-varying unit hydrograph (DTDUH) was proposed based on a time-varying unit hydrograph (TDUH). The DTDUH is a standard hydrograph representing direct runoff generated from one centimeter of effective rainfall applied uniformly over a saturated drainage basin for a specific duration. The DTDUH was computed using saturated regions of the watershed rather than the entire watershed. The saturated regions were extracted using the Topographic Wetness Index (TWI). Finally, the Longhu and Dongshi rivers were selected as two case studies. The results indicated that the proposed method exhibited consistent or better performance than the linear reservoir routing method and performed better than the TDUH method. The proposed method can be used for watersheds with sparse gauging stations and limited observed rainfall and runoff data, as with the TDUH method. Simultaneously, it applies to humid or mountain watersheds with dominant saturation-excess rainfall.</p>