Based on the ground and sounding meteorological data, the hydrological changes of the Aksu River Basin during 1960-2015 were analyzed, and the role of upper atmosphere climate in runoff reproducing was discussed. The results show that under the background of global warming, the surface air temperature in Aksu River Basin increased significantly with an rate of 0.18℃ /10a(ranging from -0.09 to 0.43℃ /10a), and the precipitation increased at a rate of 10.42 mm/10a(ranging from 2.23 to 21.11 mm/10a). For the climate at the upper atmosphere, the 0℃ level heights of Almaty, Yining and Kuqa generally increased, and the increase reached 88.9 m, 29.4 m and 7.2 m in 1990-2015 compared to those in 1960-1989, respectively. The combination of near surface air temperature and precipitation and upper 0℃ level heights can significantly improve the reproducing performance of summer runoff in the Aksu River Basin.