Qilian Mountain is an important ecological security barrier of Western China，and also an important water conservation area for the Yellow River and many inland rivers. Based on monitoring data of the sky-ground integrated monitoring system of the Qilian “mountain-river-forest-field-lake-grassland” system in 2019，an ecological function assessment was conducted. The main results were：（1）The proportion of forest，grassland，farmland and water bodies in the Pan-Qilian mountain area was 1：32：1：3，with the proportion of bare land the largest；the proportion of forest，grassland，farmland and water bodies in the Qilian mountain area（important for water conservation and carbon sequestration in the Pan-Qilian mountains area）was 6：107：1：12；（2）Mean net primary productivity（NPP）in the Qilian Mountains was about 84.42 gC/m2/a，of which forest was the highest，reaching 274.54 gC/m2/a，followed by farmland，wetland，grassland and bare land；（3）Total carbon sequestration in the whole region was c. 152 TgC，with the highest carbon sequestration per unit area in Datong River-Huangshui watershed and Qinghai Lake Basin（high carbon sequestration function）；total carbon sequestration in the Qilian mountain area was about 32.45 TgC，of which the grassland ecosystem accounted for about 50.8%；total carbon sequestration in Qilian Mountain National Park was about 7.48 TgC，also mainly from grassland；（4）Mean annual precipitation in the whole Qilian Mountains region was 318.8mm，making it a dry year. Annual evapotranspiration of different ecosystems ranged from 128 to 916 mm，the highest was in reed wetland and the lowest in Reaumuria songarica desert. Soil moisture over the whole region was in deficit. These results provide a scientific basis and data support for further understanding of the ecological function of the Qilian Mountains “mountain-river-forest-field-lake-grassland” system，and can assist green development of the Pan-Third Pole.