The spatial and temporal variation and uncertainty of precipitation and runoff in China were compared and evaluated between historical and future periods under different climate change scenarios. The precipitation pattern is derived from observed and future projected precipitation data for historical and future periods, respectively. The runoff is derived from simulation results in historical and future periods using a dynamic global vegetation model (DGVM) forced with historical observed and global climate models (GCMs) future projected climate data, respectively. One GCM (CGCM3.1) under two emission scenarios (SRES A2 and SRES B1) was used for the future period simulations. The results indicated high uncertainties and variations in climate change effects on hydrological processes in China: precipitation and runoff showed a significant increasing trend in the future period but a decreasing trend in the historical period at the national level; the temporal variation and uncertainty of projected precipitation and runoff in the future period were predicted to be higher than those in the historical period; the levels of precipitation and runoff in the future period were higher than those in the historical period. The change in trends of precipitation and runoff are highly affected by different climate change scenarios. GCM structure and emission scenarios should be the major sources of uncertainty.