The VIP eco-hydrological model and HIMS model were used to simulate hydrological processes from 1957 to 2012. Based on the ensemble projections of CMIP5 RCP2.6, RCP4.5 and RCP8.5 scenarios, the runoff in the two basins were predicted. The results show that in the past 50 years air temperatures in the two basins were continually increasing and the rates over the upstream plateau were higher than the lower downstream. The tendency of annual precipitation was not significant, while the precipitation in spring season was increasing. The total water resources were around 65 billion to 85 billion m~3 and no noticeable tendency was detected. Spatially, the water resources kept the pattern of higher in south and lower in north. The variability of water resources in Lancang River was more significant than that of Nujiang River. In the future climate scenarios, it will become warmer and wetter, the runoff will increase with lower spatial variability. Being with high seasonal variability, there will still be challenges in the water resources security over the whole basins.