We investigate the changes at nine glaciers in the Ningchan and Shuiguan river source, eastern Qilian Mountains, between 1972 and 2010. According to analysis of topographic maps and multispectral satellite data, all nine glaciers in the study area have retreated, by a maximum of 250 ± 57.4 m and a minimum of 91 ± 57.4 m. The total glacier area decreased by 1.20 km2, corresponding to 9.9% of the glacierized area in 1972. Comparing the two DEMs generated from the topographic maps and Real-Time Kinematic GPS data, the mean glacier thinning rate was 0.64 m yr− 1 between 1972 and 2010. The most significant thinning generally occurred on the termini. The ice-volume loss was about 106.8 ± 46.7 × 10− 3 km3 (equal to 90.8 ± 39.7 × 10− 3 km3 w.e.), which suggested a mean water discharge of 0.1 ± 0.05 m3/s during 1972–2010. Based on analysis of meteorological data, the summer temperature (June–August) tends to increase over a similar time period. The consistency of temperature increase and glacier shrinkage allows us to suggest that air temperature plays an important role in glacier changes in this region.