Climate change is a global issue that draws widespread attention from the international society. As an important component of the climate system, the water cycle is directly affected by climate change. Thus, it is very important to study the influences of climate change on the basin water cycle with respect to maintenance of healthy rivers, sustainable use of water resources, and sustainable socioeconomic development in the basin. In this study, by assessing the suitability of multiple General Circulation Models (GCMs) recommended by the Intergovernmental Panel on Climate Change, Statistical Downscaling Model (SDSM) and Automated Statistical Downscaling model (ASD) were used to generate future climate change scenarios. These were then used to drive distributed hydrologic models (Variable Infiltration Capacity, Soil and Water Assessment Tool) for hydrological simulation of the Yangtze River and Yellow River basins, thereby quantifying the effects of climate change on the basin water cycle. The results showed that suitability assessment adopted in this study could effectively reduce the uncertainty of GCMs, and that statistical downscaling was able to greatly improve precipitation and temperature outputs in global climate mode. Compared to a baseline period (1961–1990), projected future periods (2046–2065 and 2081–2100) had a slightly decreasing tendency of runoff in the lower reaches of the Yangtze River basin. In particular, a significant increase in runoff was observed during flood seasons in the southeast part. However, runoff of the upper Yellow River basin decreased continuously. The results provide a reference for studying climate change in major river basins of China.