We analyzed a 2-year time series of meteorological data (January 2011–December 2012) from three automatic weather stations on Laohugou glacier No. 12, western Qilian Mountains, China. Air temperature, humidity and incoming radiation were significantly correlated between the three sites, while wind speed and direction were not. In this work, we focus on the effects of clouds on other meteorological parameters and on glacier melt. On an average, ~18% of top-of-atmosphere shortwave radiation was attenuated by the clear-sky atmosphere, and clouds attenuated a further 12%. Most of the time the monthly average increases in net longwave radiation caused by clouds were larger than decreases in net shortwave radiation but there was a tendency to lose energy during the daytime when melting was most intense. Air temperature and wind speed related to turbulent heat flux were found to suppress glacier melt during cloudy periods, while increased water vapor pressure during cloudy days could enhance glacier melt by reducing energy loss by latent heat. From these results, we have increased the physical understanding of the significance of cloud effects on continental glaciers.