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Climate change and the impacts on hydrological processes in Karakoram region are highly important to the available water resources in downstream oases. In this study, a modified quantile perturbation method (QPM), which was improved by considering the frequency changes in different precipitation intensity ranges, and the Delta method were used to extract signals of change in precipitation and temperature, respectively. Using a historical period (1986-2005) for reference, an average ensemble of 18 available Global Circulation Models (GCMs) indicated that the annual precipitation will increase by 2.9-4.4% under Representative Concentration Pathway 4.5 (RCP4.5) and by 2.8-7.9% in RCP8.5 in different future periods (2020-2039, 2040-2059, 2060-2079 and 2080-2099) due to an increased intensity of extreme precipitation events in winter. Compared with the historical period, the average ensemble also indicated that temperature in future periods will increase by 0.31-0.38 degrees C/10a under RCP4.5 and by 0.34-0.58 degrees C/10a under RCP8.5. Through coupling with a well-calibrated MIKE SHE model, the simulations suggested that, under the climate change scenarios, increasing evaporation dissipation will lead to decreased snow storage in the higher altitude mountain region and likewise with regard to available water in the downstream region. Snow storage will vary among elevation bands, e.g., the permanent snowpack area below 5600 m will completely vanish over the period 2060-2079, and snow storage in 5600-6400 m will be reduced dramatically; however, little or no change will occur in the region above 6400 m. Warming could cause stronger spring and early summer stream runoff and reduced late summer flow due to a change in the temporal distribution of snowmelt. Furthermore, both the frequency and intensity of flooding will be enhanced. All the changes in hydrological processes are stronger under RCP8.5 than those under RCP4.5. In Karakoram region, the transformations among different forms of water resources alter the distributions of hydrologic components under future climate scenarios, and more studies are needed on the transient water resources system and the worsening of flood threats in the study area.