Glaciers provide essential resources and services for human well-being and socio-economic development in arid regions. It is of great significance for regional socio- economic sustainable development and environmental protection to conduct a glacier service value assessment and to analyze its spatiotemporal characteristics. Based on the first and second Chinese glacier inventories of the Qilian Mountains, a glacier service value evaluation system was established. Then the glacier service value and its spatiotemporal variation were assessed by combining the methods of unit area service price, value equivalent factor, and the glacier service value change index (GSCI). Three key results were obtained. (1) The total service value of glaciers in the Qilian Mountains for 2016 was 24.354 billion yuan. The main services provided were climate regulation and runoff regulation, which accounted for 60.58% and 33.14% of the total service value, respectively. Minor services were freshwater supply and hydropower, which accounted for 3.47% and 1.75% of the total value, respectively. The value of other types of services was about 0.259 billion yuan. (2) Among the various river systems in the Qilian Mountains, the Shule River basin had the highest glacier service value (7.771 billion yuan, 31.91%), followed by the Haltang River basin (4.321 billion yuan, 17.74%) and the Beida River basin (3.281 billion yuan, 13.47%). In terms of administrative divisions, the glacier service value of the Qilian Mountains in Qinghai Province was 1.138 billion yuan higher than that of Gansu Province at 11.608 billion yuan, of which the services in the Haixi Mongol and Tibetan Autonomous Prefecture and Jiuquan City were valued at 11.124 (45.68%) and 7.758 (31.86%) billion yuan, respectively. (3) During the period from 1956 to 2010, the service value of glaciers in the Qilian Mountains declined by 435 million yuan, with an acceleration in the decreasing trend from west to east.