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Baseflow is an essential component of river runoff. Accurate measurements and analyses of baseflow change are challenging in permafrost-covered regions. In this paper, the upper reaches of the Shule River were selected as the study area, in which to study the baseflow change regulation and causes. The variable infiltration capacity (VIC) model, based on the ARNO baseflow formulation, was used to simulate the baseflow. Simulated baseflow was validated by the isotopic baseflow separation results and measured runoff in the recession periods throughout an entire year. It was found that approximately 63.1% of the river runoff was sourced by baseflow in the study region; the baseflow change was relatively smooth throughout the year, and it lagged a few days behind the river runoff. Approximately 80% of the total baseflow was generated in the 3500-4500 m alpine regions, with mainly low-temperature and mid-temperature permafrost. Based on the climate, runoff, land use, soil temperature and moisture data of the permafrost active layer, the mechanism of baseflow change in the permafrost zone was analysed. Precipitation and temperature positively enhanced the baseflow in the permafrost region throughout a year, but the baseflow was more influenced by the temperature than precipitation. In the study area, the cold desert and alpine grassland had the largest regulation capacity for baseflow. Affected by the permafrost freeze-thaw process, a baseflow peak occurred in the spring and the baseflow recession slowed in the autumn. This lead to a more uniform distribution of baseflow and runoff throughout the year.