This study focused on the hydrological and runoff formation processes of river water by using stable isotope tracing in the source regions of the Yangtze River during different ablation episodes in 2016 and the ablation period from 2016 to 2018. The effects of altitude on stable isotope characteristics for the river in the glacier permafrost area were greater than for the main stream and the permafrost area during the ablation period in 2016. There was a significant negative correlation (at the 0.01 level) between precipitation and δ18O, while a significant positive correlation was evident between precipitation and d-excess. More interestingly, significant negative correlations appeared between δ18O and temperature, relative humidity, and evaporation. A mixed segmentation model for end-members was used to determine the proportion of the contributions of different water sources to the target water body. The proportions of precipitation, supra-permafrost water, and glacier and snow meltwater for the main stream were 41.70%, 40.88%, and 17.42%, respectively. The proportions of precipitation, supra-permafrost water, and glacier and snow meltwater were 33.63%, 42.21%, and 24.16% for the river in the glacier permafrost area and 20.79%, 69.54%, and 9.67%, respectively, for that in the permafrost area. The supra-permafrost water was relatively stable during the different ablation periods, becoming the main source of runoff in the alpine region, except for precipitation, during the ablation period.
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