Abstract: According to the air temperature and precipitation from the projection of IPCC fifth assessment report (AR5), an estimation model of annual runoff is presented in this paper. As an example, the variabilities of annual runoff in the upper reaches of Yangtze River are studies under the different future climate change scenarios of 5 GCMs, which have been analyzed and applied in the IPPC AR5. The results show that the annual runoff time series is a non-significant tendency under the RCP2.6and RCP4.5 scenario, while there is a significant deceasing trend for the annual runoff time series under the RCP8.5 scenario during the period of 2020～2099 at the 99% confidence level. On the other hand, under the RCP2.6, RCP4.5 and RCP8.5 scenario, the decrease in average annual runoff from 2020 to 2099 is 6.42%, 10.99% and 13.25% respectively compared with that of 1961～2000. The work aids understanding of the climate of the upper reaches of Yangtze River under global warming and provides information for regional planning and management of water resources.