The flow regime is of vital importance for the sustainable development of both human society and aquatic biota. Alterations in natural streamflow will modify the stability and biophysical distribution of river conditions, causing a series of adverse ecological and economic consequences. Climate change has been proven to pose potential threats to ecosystems; however, few studies have been conducted to quantify the variations between the flow regime of a future period and pristine natural flow specifically. This study investigates the future impacts induced by the changing climate in the Jinsha River Basin, which is known as the “Asian Water Tower” due to its rich hydroelectric energy resources. The SWAT model is used and calibrated to predict future streamflow. Seven GCMs from NASA NEX-GDDP with one ensemble average under two RCPs (RCP4.5 and RCP8.5) are used for both the NFP (2040s) and the FFP (2080s). The Indicators of Hydrologic Alteration (IHA) software and the river regime index (RRI) are used to assess the potential flow alterations of the Jinsha River. The results show that Pr, Tmax and Tmin all denote increasing trends, with the temperature trends being more obvious. For interannual alterations in flow regimes, most IHA values show moderate and high changes in all predicted conditions. In regard to the intra-annual changes, the results of the RRI show that river flow tends to be more concentrated in wet seasons than in cold seasons and denote evident seasonality and transience with advanced overall peaks of the river system. These findings together indicate that the flow patterns may have noticeable changes corresponding to the natural river regime.