To investigate and monitor permafrost in the Bayan Har Mountains (BHM), north‐eastern Qinghai–Tibet Plateau, southwest China, 19 boreholes ranging from 20 to 100 m in depth were drilled along an elevational transect (4,221–4,833 m a.s.l.) from July to September 2010. Measurements from these boreholes demonstrate that ground temperatures at the depth of zero annual amplitude (TZAA) are generally higher than −2.0°C. The lapse rates of TZAA are 4 and 6 °C km−1, and the lower limits of permafrost with TZAA < −1°C are approximately 4,650 and 4,750 m a.s.l. on the northern (near Yeniugou) and southern (near Qingshui'he) slopes, respectively. TZAA changes abruptly within short distances from −0.2 to +1.2°C near the northern lower limits of permafrost and from about +0.5 to +1.5°C near the southern lower limits of permafrost. Thawing and freezing on the ground surface at Qingshui'he (4,413 m a. s. l.) are 13.3 d earlier and 26 d later than that at Chalaping (4,724 m a. s. l.), respectively. The temperature gradient at Qingshui'he is clearly larger than that at Chalaping. The changes of permafrost TZAA ranged from 0.03°C to 0.2°C from 2010 to 2017. A 3.5‐m‐thick permafrost near Qingshui'he was observed to disappear in summer 2013. There is no significant correlation between elevation and permafrost temperature changes in the study area, whereas the changes of very warm (close to 0°C) permafrost seem to be slow in the intermontane basins.