A regional climate model (RegCM3) nested in one-way mode within a NASA/NCAR finite volume element AGCM (FvGCM) is used in this study. Two sets of multi-decadal simulations are conducted at 20-km grid spacing for present day (1961-1990) and future climates (2071-2100, A2 scenario). The runoff outputs are used to drive a large-scale routing model (resolution, 0.25°×0.25°), to project the effect of future climate change on hydrological extreme events over the Yellow River and Yangtze River basins. The results show that the annual variability of the streamflow over the Yellow River will increase, and the monthly variability will decrease. The diurnal variability will decrease upstream and increase downstream of Toudaoguai station. A greater possibility of the largest streamflow percentile will exist in the upper reaches of Lanzhou station in sub-humid areas and southeast of the Yellow River basin in humid areas, whereas the possibility is less in the arid and semi-arid areas of the northwestern basin. The flood disaster risk will increase in future over the middle reaches of the Yellow River except in the summer season. The annual variability of the Yangtze River may increase, and the diurnal and monthly variability may decrease in the upper and middle reaches and rise slightly in the lower reaches in future. The annual, monthly, and diurnal variability of the streamflows all increase in future over the Hanjiang River basin. The flood disaster risk may decrease over the Yangtze River, especially in summer, and the probability of flooding in the Hanjiang River basin will increase in each month.