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Soil hydrothermal dynamics, resulting from the freezing and thawing processes in the active layer and their influencing factors, were studied in the upper Heihe River Basin (UHRB) in the Qilian Mountains, northeastern Tibetan Plateau. Soil temperature and water content measurements were taken in the active layer of the UHRB in alpine grassland from 2013 to 2014. The results showed that the thaw rate of the active layer was significantly smaller in alpine paludal meadows than the thaw rate in alpine meadows and alpine steppes. This was mainly related to the hydrothermal properties of soils in the active layer, such as moisture content, thermal conductivity, and specific heat. During the thawing process, the active layer soil water content was higher and fluctuated less in alpine paludal meadows. Conversely, the soil water content was lower and fluctuated more significantly in alpine meadows and alpine steppes. These findings could be explained by the prevalence of peat soils, with a low bulk density, and high clay and organic matter content. By contrast, the soil particles in the active layer of alpine meadows and alpine steppes were significantly coarser, with higher bulk density and lower organic matter content. During the freezing process, gravel content and soil texture had a great impact on the unfrozen water content in the frozen soils. However, the factors influencing the soil water retention in frozen soils are complex, and further study is needed. These results provide theoretical support for the evaluation of the hydrological characteristics of the alpine permafrost zone in the Qilian Mountains. Furthermore, the effect of frozen ground on hydrological changes due to climate change in the Heihe River Basin can be simulated and predicted, providing a scientific basis for the ecological conservation of the Qilian Mountains National Park.