Because of the special geographical environment such as glaciers and permafrost in the western alpine area of China, the simulation and prediction of its runoff process has been one of the difficult and hot spot issues in hydrological research. In addition, the global warming has raised a new challenge for hydrological simulation in this area. In this study, based on the SWAT model which considers the melting process of the glaciers and snow packs, the runoff process above the Lazi Station in the upstream of the Yarlung Zangbo River was simulated and the applicability of the SWAT model to the alpine area was also evaluated. Eighteen GCMs from Coupled Model Intercomparison Project Phase 5 under three Respectively Concentration Pathways (RCP2.6, RCP4.5 and RCP8.5) were used to assess the impact of climate change on precipitation, temperature and streamflow above the Lazi Station in the upstream of the Yarlung Zangbo River. The results show that the SWAT model has better applicability in simulating runoff process, and the monthly scale Nash -Sutcliffe Efficiencies (NS) are 0.78 and 0.84 for the calibration and validation periods respectively. Besides, both the precipitation and temperature show an increasing trend in the period of 2020-2049, and both factors present a more significantly rising trend with the rise of the emission scenario. Moreover, the runoff in different durations also shows different increasing trends. The runoff increased by about 11.8%, 14.0%, and 16.5% compared to the baseline runoff under the scenarios of RCP2.6, RCP4.5 and RCP8.5 during the period of 2020-2049.