Abstract: Runoff in the Upper Yarkant River Basin is strongly influenced by glacier and snow meltwater, yet their long-term contributions and regulatory effects remain insufficiently quantified. The SPHY model was therefore applied to simulate and partition runoff during 1962—2022 using CN05.1 daily meteorological data, MODIS snow-cover fraction data, glacier inventory data, and observed runoff records from the Kaqun hydrological station. The results showed that annual runoff depth increased significantly at a rate of 9.2 mm per decade. This increase was mainly driven by significant increases in glacier-melt runoff and rainfall runoff, at rates of 4.9 and 4.2 mm per decade, respectively, whereas snowmelt runoff exhibited no significant trend. On average, glacier-melt, snowmelt, rainfall runoff, and baseflow contributed 62.2%, 18.5%, 13.3%, and 6.0% of total runoff, respectively. The relative contributions of these runoff components remained largely stable across different hydrological year types. Sensitivity experiments revealed that increases in air temperature of 1 ℃ and 2 ℃ would increase annual runoff depth by 19.9% and 42.6%, respectively, while precipitation increases of 10% and 20% would enhance runoff by 5.7% and 12.0%. In contrast, reductions in glacier area of 5%, 10%, and 20% would decrease annual runoff depth by 11.7%, 18.3%, and 28.4%, respectively. Overall, runoff in the Upper Yarkant River Basin was persistently controlled by glacier-melt, although the rainfall runoff contributions have increased in recent decades. Continued glacier retreat is expected to weaken meltwater supply and reduce the basin’s runoff-regulation capacity during the ablation season. These findings provide a scientific basis for assessing future changes in glacier and snow meltwater and for developing adaptive water-resources management strategies in the Upper Yarkant River Basin.