To assess the impacts of climate change on river runoff in the upper Yangtze River basin, the climate change and its impacts on spatial-temporal trend of annual, seasonality and extremes of runoff were examined using Soil and Water Assessment Tool (SWAT) model, based on a subset of five global circulation models under three Representative Concentration Pathways (RCP2.6, RCP4.5, RCP8.5). The projected average annual temperature presents a significant upward trend, with an increase of 1.5-5.5 ℃ by the end of the 21st century relative to the reference period 1986-2005, and the overall precipitation is projected to increase after 2030s, with an increase of 5%-15% by the end of the 21st century. There is considerable spatial variation in the projected changes in annual temperature and precipitation across the upper Yangtze River basin, with the upper sub-basins (Jinsha River and Mintuo River) having a generally warmer and wetter conditions comparing with the whole study area. Changes of climate will result in an increase in the simulated mean annual runoff in the upper Yangtze River basin after 2030s, with an increase of 4%-8% in middle of the 21st century, and 10%-15% increase by the end of the 21st century. Additionally, the intra-annual distribution of monthly runoff is simulated generally more uniform. However, the inter-annual variation of runoff is simulated to increase, which indicates more frequent and severe extreme flood and drought events. With respect to spatial differences in simulated runoff, the sub-basins of Jinsha River and Mintuo River show a relative small change in the annual water availability as well as the inter-annual and intra-annual variability, whereas the sub-basins of Jialing, Wujiang, and mainstream of the upper Yangtze River show a larger increase in water availability and hydrological extremes.