Against the background of climate change, alpine permafrost active layers have shown a gradual thickening trend and the hydrothermal conditions have undergone significant changes in the Tianshan Mountains and the Qinghai-Tibet Plateau, China. At the ice-free cirque basins in the headwaters of the Urumqi River(hereafter referred to as the Ice-Free Cirque) in eastern Tianshan, China, the hydrological effects of the alpine permafrost active layers appear to have also exhibited significant changes recently. The increasing trend of local precipitation is clear in May and June. The onset of winter and spring snowmelt runoff clearly lags behind increases of air temperature, and the runoff peak appears near the beginning of the melting season, which results in the spring runoff increasing. In summer, runoff decreases strongly and the maximum runoff occurs earlier. In our analysis of meteorological and hydrologic data from 1959 to 2010, the runoff and precipitation changes are significantly correlated. In the initial stage of runoff, the runoff-producing process is mainly under the control of the soil water content and soil temperature in the 0–30 cm active layers. Spring precipitation and snowmelt water are mainly involved in the processes of infiltration and evaporation while some melt water infiltrates into the seasonal thawed layer and stays above the frozen layers. During the strong ablation period in summer, the runoff-generating process is mainly controlled by soil water content in the active layers deeper than 60 cm. In the active layer, precipitation and seasonal snowmelt water infiltrates, migrates, collects, and then forms runoff. Against the background of climate change, alpine permafrost active layers have shown a gradual thickening trend and the hydrothermal conditions have undergone significant changes in the Tianshan Mountains and the Qinghai-Tibet Plateau, China. At the ice-free cirque basins in the headwaters of the Urumqi River (hereafter referred to as the Ice-Free Cirque) in eastern Tianshan, China, the hydrological effects of the alpine permafrost active layers appear to have also presented significant obvious recently recently. The increasing trend of local precipitation is clear in May and June. The onset of winter and spring snowmelt runoff clearly lags behind increases of air temperature, and the runoff peak appears near the beginning of the melting season, which results in the spring runoff increasing. In summer, runoff decreased strongly and the maximum runoff occurred earlier. In our analysis of meteorological and hydrologic data from 1959 to 2010, the runoff and precipitation changes are significantly cor related. In the initial stage of runoff, the runoff-producing process is mainly under the control of the soil water content and soil temperature in the 0-30 cm active layers. Spring precipitation and snowmelt water are mainly involved in the processes of infiltration and during the strong ablation period in summer, the runoff-generating process is mainly controlled by soil water content in the active layers more than 60 cm. In the active layer, precipitation and seasonal snowmelt water infiltrates, migrates, collects, and then forms runoff.