The source region of Yellow river is an alpine river sensitive to climate changes, but the potential effects of climate change on hydrological regime characteristics and ecological implications are less understood. This study aims to assess the response of the alterations in the flow regimes over the source region of Yellow river to climate change using Soil and Water Integrated Model driven by different Global Circulation Models (GFDL-ESM2M, IPSL-CM5A-LR and MIROC-ESM-CHEM) under three Representative Concentration Pathway emission scenarios (RCP2.6, RCP4.5 and RCP8.5). Indicators of hydrological alteration and River impact index are employed to evaluate streamflow regime alterations at multiple temporal scales. Results show that the magnitude of monthly and annual streamflow except May, the magnitude and duration of the annual extreme, and the number of reversals are projected to increase in the near future period (2020–2049) and far future period (2070–2099) compared to the baseline period (1971–2000). The timing of annual maximum flows is expected to shift backwards. The source region of Yellow river is expected to undergo low change degree as per the scenarios RCP2.6 for both two future periods and under the scenarios RCP4.5 for the near future period, whereas high change degree under RCP4.5 and RCP8.5 in the far period on the daily scale. On the monthly scale, climate changes mainly have effects on river flow magnitude and timing. The basin would suffer an incipient impact alteration in the far period under RCP4.5 and RCP8.5, while low impact in other scenarios. These changes in flow regimes could have several positive impacts on aquatic ecosystems in the near period but more detrimental effects in the far period.