As an important ecological security barrier in western China，Qilian Mountains are an important water source of the Yellow River and many inland rivers. Based on the integrated monitoring data set of the “Mountains，Water，Forests，Farmlands，Lakes and Grasslands” system in Qilian Mountains，this study evaluated the ecological function of the “Mountains，Water，Forests，Farmlands，Lakes and Grasslands” system in 2020. The main results are as follows：（1）The ratio of forests：grasslands：farmlands：water in Pan-Qilian Mountains is 1∶44∶1∶2，with bare lands contributing the most. And the ratio in Qilian mountains is 2∶115∶1∶14. Compared with the Pan-Qilian Mountains，the proportion of forests，grasslands and water bodies in Qilian Mountains have all increased significantly，which means Qilian Mountains are an important water-conserving and carbon-fixing functional area in the Pan-Qilian Mountains. （2）The mean net primary productivity of Qilian Mountains in 2020 is about 98.96gC/m2/a，with forests being the highest at 312.03gC/m2/a，followed by farmlands，wetlands，grasslands，shrubs and bare lands. （3）The total carbon sequestration of the Pan-Qilian Mountains in 2020 is about 197.81TgC. Datong River-Huangshui Basin has the highest carbon sequestration per unit area，followed by Qinghai Lake Basin，which is an important carbon sequestration functional area. The carbon sequestration of Qilian Mountains in 2020 is 35.78TgC，with grasslands ecosystem accounting for 74.72%. The total carbon sequestration of Qilian Mountain National Park in 2020 is about 8.12TgC，of which grasslands are the main carbon sequestration. （4）The average rainfall of the Pan-Qilian Mountains in 2020 is 195.1mm，which is a dry year. The annual evapotranspiration of different ecosystems ranges from 29.0 mm to 1163.0mm，with the highest in reed wetland and the lowest in Reaumuria soongrica desert. Soil moisture is in a deficit state throughout the region，with low soil water storage and low flow production. These results provide scientific basis and data support to understand the ecological function of “Mountains，Water，Forests，Farmlands，Lakes and Grasslands” system in Qilian Mountains，which can support the green development of pan-Third Pole.