Within the gas hydrate drilling project in the Qilian Mountain permafrost region, a temperature–depth profile measured from borehole DK-12 in Juhugeng of Muri Coalfield, Tianjun County, Qinghai Province, China, was analyzed to infer recent climate changes. The long-term surface temperature and thermal gradient were retrieved from borehole temperature measurements. The ground surface temperature (GST) changes were reconstructed by inversion of transient temperature perturbations through solving an inverse heat conduction problem using the Tikhonov method. Based on the instability of this kind of inverse problem and the nature of method-dependent features of borehole paleothermometry, we initially applied the Tikhonov regularization technique to obtain a stable past GST variation pattern with relatively low resolution. The inversion results showed that this region experienced temperature fluctuation with a total warming of 3°C (±1.6°C) from 1400 to the 2010s and a more exacerbated warming starting from the 1960s. The GST trend fit the surface air temperature observation trend from the nearest Yeniugou meteorological station. This work fills the gap created by limited meteorological records in the Muli area and extends knowledge of ground surface temperature trends going back more than ten centuries. © 2020 The Author(s). Published with license by Taylor & Francis Group, LLC.