With global warming, hydrological regimes in the headwater basins of the Tibetan Plateau (TP) have significantly changed. Investigating the responses of hydrological processes to climate change in TP has become more and more important to make robust strategies for water resources management. However, using just a few GCMs may constrain the uncertainty in assessment of climate impacts. Therefore, a framework is proposed in this study to generate ensemble climate change scenarios and then investigate changes of hydrological processes under climate change in the upper reaches of Yarlung Zangbo River basin (UYZR) and Lancang River basin (ULR). Firstly, the Latin Hypercube Simulation (LHS) is used to generate an ensemble of future climate change scenarios by resampling change factors of meteorological variables from 18 GCMs under emission scenarios RCP2.6 and RCP8.5. The inherent dependence structures of change factors, i.e. the correlations of change factors among 12 months for different meteorological variables, are also considered in ensembles. Secondly, the HBV hydrological model coupled with a degree-day snowmelt model is applied to explore the potential change of runoff in the future period 2041-2070. Results show that: 1) the resampling method is effective and can provide a wide ensemble of climate change scenarios. 2) Precipitation, temperature and potential evapotranspiration in the UYZR and ULR basins are expected to increase under the two scenarios, particularly under RCP8.5. 3) The total runoff also shows a moderately upward trend in two basins, both mainly due to increased precipitation. In the UYZR basin, fast runoff accounts for a larger proportion in total runoff than slow runoff, while in ULR, both almost play the same role in total runoff. Furthermore, snowmelt-induced runoff in both basins would be less and rainfall-induced runoff will probably become more important in the future.