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Warming permafrost on a global scale is projected to have significant impacts on engineering, hydrology and environmental quality. Greater warming trends are predicted on the Qinghai-Tibetan Plateau (QTP), but most models for mountain permafrost have not considered the effects of water phase change and the state of deep permafrost due to a lack of detailed information. To better understand historical and future permafrost change based on in situ monitoring and field investigations, a numerical heat conduction permafrost model was introduced which differentiated the frozen and thawed state of soil, and considered unfrozen water content in frozen soil, distribution of ground ice and geothermal heat flow. Simulations were conducted at two sites with validation by long-term monitoring of ground temperature data. After forcing with reconstructed historical ground surface temperature series starting from 1966, the model predicted permafrost changes until 2100 under different RCP scenarios. The results indicate a slow thermal response of permafrost to climate warming at the two investigated sites. Even under the most radical warming scenario (RCP8.5), deepening of the permafrost table is not obvious before 2040. At both sites, the model indicates that shallow permafrost may disappear but deep permafrost may persist by 2100. Moreover, the simulation shows that the degradation modes may differ between zones of discontinuous and continuous permafrost. The main degradation mode of the site in the discontinuous zone appears to be upward thawing from the permafrost base, while that of the site in the continuous zone is downward thawing at the permafrost table with little change at the permafrost base.