Glaciers in the Qilian Mountains, China, play an important role in supplying freshwater to downstream populations, maintaining ecological balance, and supporting economic development on the Tibetan Plateau. Glacier snowline altitude (SLA) at the end of the melt season is an indicator of the Equilibrium line altitude (ELA), and can be used to estimate the mass balance and climate reconstruction. Here, we employ the height zone-area method to determine the SLA at the end of the melt season during the 1989–2018 period using Landsat, MODIS (Moderate Resolution Imaging Spectroradiometer) SLA and Shuttle Radar Topography Mission (SRTM) digital elevation model (DEM) data. The accuracy of glacier SLA obtained in 1989–2018 after adding MODIS SLA data to the years without Landsat data increased by about 78 m. The difference between the remote-sensing-derived SLA and measured equilibrium line altitude (ELA) is mostly within 50 m, suggesting that the SLA can serve as a proxy for the ELA at the end of the melt season. The SLA of Qiyi Glacier in the Qilian Mountains rose from 4690 ± 25 m to 5030 ± 25 m, with an average of 4900 ± 103 m during the 30 year study period. The western, central, eastern sections and the whole range of the Qilian Mountains exhibited an upward trend in SLA during the 30 year study period. The mean glacier SLAs were 4923 ± 137 m, 4864 ± 135 m, 4550 ± 149 m and 4779 ± 149 m for the western, central, eastern sections and the whole range, respectively. From the perspective of spatial distribution, regardless of the different orientation, grid scale and basin scale, the glacier SLA of Qilian Mountains showed an upward trend from 1989 to 2018, and the glacier SLA is in general located at a comparably higher altitude in the southern and western parts of the Qilian Mountains while it is located at a comparably lower altitude in its northern and eastern parts. In an ideal condition, climate sensitivity studies of ELA in Qilian Mountains show that if the summer mean temperature increases (decreases) by 1 °C, then ELA will increase (decrease) by about 102 m. If the annual total solid precipitation increases (decreases) by 10%, then the glacier ELA will decrease (rise) by about 6 m. The summer mean temperature is the main factor affecting the temporal trend of SLA, whereas both summer mean temperature and annual total precipitation influence the spatial change of SLA.