Warming in mountainous areas has obvious elevation dependence (warming rate increases with elevation), which deeply impacts runoff change in mountainous areas. This study analysed the influence of elevation-dependent warming on runoff in the headwater region of the Urumqi River Basin (URB) based on meteorological data, remote sensing images, and runoff data. Results indicated a significant warming rate in the URB from 1960 to 2019 (0.362 °C/decade; p < 0.01). The temperature increased with an obvious elevation-dependent warming in the URB, especially during winter. Glaciers sharply retreated in the headwater region of the URB under regional warming, and remote-based results showed that glacier areas decreased by 29.45 km² (−57.81%) from the 1960s to 2017. The response of glacier mass balance and meltwater runoff to temperature change has a lag of 3 years in the headwater region of the URB. The elevation-dependent warming of temperature changes significantly impacted glacial meltwater runoff in the URB (R² = 0.49). Rising temperatures altered the glacial meltwater runoff, and the maximum annual runoff of the Urumqi Glacier No. 1 meltwater runoff increased 78.6% in 1990–2017 compared to 1960–1990. During the period of 1960–1996, the total glacial meltwater runoff amounted to 26.9 × 10⁸ m³, accounting for 33.4% of the total runoff during this period, whereas the total glacial meltwater runoff accounted for 51.1% of the total runoff in 1996–2006. Therefore, these results provide a useful reference for exploring runoff changes in mountainous watersheds in the context of elevation-dependent warming.