Floods are one of the most common natural hazards occurring all around the world. However, the knowledge of the origins of a food and its possible magnitude in a given region remains unclear yet. This lack of understanding is particularly acute in mountainous regions with large degrees in Sichuan Province, China, where runoff is seldom measured. The nature of streamflow in a region is related to the time and spatial distribution of rainfall quantity and watershed geomorphology. The geomorphologic characteristics are the channel network and surrounding landscape which transform the rainfall input into an output hydrograph at the outlet of the watershed. With the given geomorphologic properties of the watershed, theoretically the hydrological response function can be determined hydraulically without using any recorded data of past rainfall or runoff events. In this study, a kinematic-wave-based geomorphologic instantaneous unit hydrograph (KW-GIUH) model was adopted and verified to estimate runoff in ungauged areas. Two mountain watersheds, the Yingjing River watershed and Tianquan River watershed in Sichuan were selected as study sites. The geomorphologic factors of the two watersheds were obtained by using a digital elevation model (DEM) based on the topographic database obtained from the Shuttle Radar Topography Mission of US's NASA. The tests of the model on the two watersheds were performed both at gauged and ungauged sites. Comparison between the simulated and observed hydrographs for a number of rainstorms at the gauged sites indicated the potential of the KW-GIUH model as a useful tool for runoff analysis in these regions. Moreover, to simulate possible concentrated rainstorms that could result in serious flooding in these areas, synthetic rainfall hyetographs were adopted as input to the KW-GIUH model to obtain the flow hydrographs at two ungauged sites for different return period conditions. Hydroeconomic analysis can be performed in the future to select the optimum design return period for determining the flood control work.