Glacier surface temperature is not only an important indicator of climate change, but is also directly related to glacier physical processes and mass balance. Glaciers over the Third Pole have shown heterogeneous but accelerated mass loss over the past two decades. However, few studies have focused on changes of glacier surface temperature in this region. In this study, we investigate this change from 2000 to 2021 using an altitudinal area-weighting method based on Landsat surface temperature products. The results show that this method can robustly derive inter-annual variability and long-term trends of subregional glacier surface temperature. Over the entire Third Pole, glacier surfaces exhibited warming at the rate of +0.17 ± 0.35 °C dec⁻¹ (p = 0.32). The warming had a distinct seasonal pattern: warming in autumn (+0.50 ± 0.53 °C dec⁻¹, p = 0.06) but cooling in spring (−0.22 ± 0.36 °C dec⁻¹, p = 0.23). Correspondingly, the ablation season 0 °C isotherm altitude has risen >100 m and the glacier area with GST ≥0 °C has expanded by 10%. Moreover, the GST changes displayed large spatial heterogeneity. In the westerlies-dominated regions (e.g., Karakoram and Kun Lun), glacier surfaces showed slight warming or even cooling on average (from −0.10 to +0.06 °C dec⁻¹), while in the monsoon-dominated regions (e.g., East Himalaya, Southeast Tibetan Plateau and Hengduan Mountains), strong warming was observed (> +0.50 °C dec⁻¹, p < 0.05). Glacier surfaces generally showed a faster warming at north slopes than south slopes, especially in the ablation season. These results emphasize that different magnitudes of glacier surface warming are important indicators for the contrasting glacier changes over the Third Pole. The method presented here opens the way to investigate long-term surface temperature change of global mountain glaciers, which can help us further understand the mechanisms of glacier response to global climate change.