Qilian Mountains, is an important ecological function area, an important ecological security barrier, the river runoff region in Northwest China, as well as a sensitive area to global climate change and fragile area of ecological environment. The ecological environment in this area played an important role in the economic development of Northwest China. Based on the observation data of temperature and precipitation in Qilian Mountains, MOD10A2 snow products and the flow data of Shiyang River, Heihe River and Shule River, we systematically analyzed the characteristics of climate change from 1961 to 2020, and the impacts of climate change on water resources under the scenario of climate warming. The results showed that, from 1961 to 2020, the annual average temperature increased significantly, with the rate reaching 0.39 ℃·(10 a) -1 . The warming rate was the highest in the western part of Qilian Mountains, followed by the middle and eastern regions. The warming trend was the strongest in winter and the lowest in spring. The average temperature changed abruptly in 1997. The annual average precipitation increased with flucturation, with a rate of 10 mm·(10 a) -1 , which increased most obviously in the middle of Qilian Mountains. After 2004, it entered a rainy period, with a warm and humid trend. The precipitation in the four seasons showed an increasing trend and the increase of precipitation in summer contributed the most to the annual precipitation. Annual precipitation was dominated by interannual scale change, and the contribution rate of 2.8-year was approximately 64.3%. The snow cover of Qilian Mountains was obviously affected by temperature and snowfall, which was negatively correlated with summer temperature and positively correlated with snowfall. From 2016 to 2020, the temperature increase had slowed down in Qilian Mountains, the snowfall had increased, and the snow cover tended to increase. After 2000, the temperature and precipitation increased more obviously, the meltwater from glacier and snow increased, the mountainous runoff of Shiyang River, Heihe River and Shule River had an increasing trend. Our findings are of great significance to the construction of ecological civilization and coping with climate change in Qilian Mountains.