The Qilian Mountains provide an ecological security barrier, and the region is an important river runoff area in China. Water resources play an essential role in the natural environment of Northwest China. This study used daily temperature and precipitation data from meteorological stations in the Qilian Mountains from 2003 to 2019, Gravity Recovery and Climate Experiment, and Moderate Resolution Imaging Spectroradiometer satellite data. Additionally, we used the Gravity Recovery and Climate Experiment satellite's monthly gravity field model data. Furthermore, we analyzed the characteristics of climate warming and humidification in the eastern, central, and western sections of the Qilian Mountains based on spatial precipitation interpolation and linear trend analysis. Finally, we examined the relationship between water storage changes and precipitation and its impact on vegetation ecology. The results revealed a significant warming and humidification trend in the western Qilian Mountains. The temperature increased significantly, and the increased precipitation rate in summer reached 1.5–3.1 mm/10a. Water storage in the Qilian Mountains displayed an increasing trend, with an increase of approximately 14.3 × 108 m3 over the 17 years study period, averaging an increase of 8.4 mm/year. The spatial distribution of water storage in the Qilian Mountains increased from north to south and east to west. There were noticeable seasonal differences, with the largest surplus occurring in the western Qilian Mountains (71.2 mm in summer). The fractional vegetation coverage in 95.2 % of the western Qilian Mountains and net primary productivity in 90.4 % of the area displayed an increasing trend, and vegetation ecology improved significantly. This study aims to investigate the characteristics of ecosystem and water storage changes in the Qilian Mountain area under the background of climate warming and humidification. The results obtained from this study provided an assessment of the vulnerability of alpine ecosystems and helped in making spatially explicit decisions for the rational utilization of water resources.