The SWAT model embedded with glacier module was built for glacier runoff simulation in the upper Hotan River Basin. Based on the measured runoff data and glacier cataloging data, the model was corrected and verified, and the contribution of glacier runoff to surface runoff, change trend of glacier runoff, and its response rule to climate change in the river basin were quantitatively analyzed. The results show that the average annual glacial runoff of the Yurungkash River Basin is 11.02×10⁸.m³, with its contribution rate to surface runoff being 48.70%, and the average annual glacial runoff of the Karakash River Basin is 9.51×10⁸.m³, with its contribution rate to surface runoff being 45.46%; with regard to the significance level of 0.01, temperature and precipitation of the Yurungkash River Basin have significant increasing trends, respectively, temperature of the Karakash River Basin has a significant increasing trend, while precipitation of the Karakash River Basin has an insignificant increasing trend; under the climate change background, there is a large difference between the runoff responses of the two tributaries due to different geographical positions and glacier characteristics, with glacier runoff of the Yurungkash River Basin and its contribution rate having a significant increasing and decreasing trend, respectively, while the glacial runoff of the Karakash River Basin and its contribution rate both having increasing trends.