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Observational data collection on permafrost and active layer freeze thaw cycle is extremely limited in the upper reaches of the Heihe River (URHHR) in the Qilian Mountains of the north-eastern Qinghai Tibet Plateau. It acts as a bottleneck, restricting the hydrological effects of the changes in the permafrost and active layer in the Heihe River Basin. Using soil temperature, moisture and air temperature data collected from the four active layer observation sites (ALl, AL3, AL4 and AL7) established in the alpine permafrost regions in the URHHR, from 2013 to 2014, the region's active layer freeze thaw cycle and the soil hydrothermal dynamics were comparatively analysed. As the elevation increased from 3700 m a.s.l. to 4132 m a.s.l., the mean annual ground temperatures (MAGTs) of the active layer and the active layer thicknesses (ALTS) decreased, the onset date of soil freeze of the active layer occurred earlier and the soil freeze rate increased. However, the onset date of soil thaw and the thaw rate did not exhibit significant trends. Compared to the thaw process, the duration of the active layer freeze process was significantly shortened and its rate was significantly higher. The soil freeze from bottom to top did not occur earlier than that from top to bottom. Furthermore, as elevation increased, the proportion of the bottom -up freeze layer thickness increased. The soil moisture in the thaw layer continuously moved to the freeze front during the active layer's two-way freeze process, causing the thaw layer to be dewatered. The seasonal thaw process resulted in significant reduction of the soil water content in the thaw layer, accounting for the high ice content in the vicinity of the permafrost table. Controlled by elevation, the active layer's seasonal freeze thaw cycle was also affected by local factors, such as vegetation, slope, water (marsh water and super -permafrost water), lithology and water (ice) content. This study provides quantitative data that identify, simulate and predict the hydrological effects of the changes in the permafrost and active layer of the Heihe River Basin. (C) 2016 Elsevier Ltd and INQUA. All rights reserved.