Baseflow is an important component of streamflow in alpine permafrost basins and plays a significant role in maintaining ecosystem security and rational planning of water resources. Meanwhile, a holistic analysis of the runoff process and determination of low-flow components helps to better understand hydrological processes in permafrost regions. In this context, an approach for determining low-flow components is presented. As a support, daily flow data regarding the source regions of the Yangtze River (YARSR) and Yellow River (YERSR) from 1965 to 2014 were divided into three groups (wet, normal, and dry years) to analyze baseflow, recession curves, and flow duration curves (FDC). The results showed that low-flow components can be determined from the corre-sponding relationship between percentile flow (Qpi) in FDC, baseflow, and recession processes. Sub-permafrost groundwater is the main component of baseflow in the permafrost regions of the Qinghai-Tibet Plateau. The multi-year average proportion of sub-permafrost groundwater in YARSR and YERSR at Q75, Q85, and Q94 ranged from 75.5% to 100%, suggesting the dominance of sub-permafrost groundwater in sustaining low-flows. In addition, river discharge in dry years was more dependent on deep groundwater. The sub-permafrost groundwater proportion in low-flows in dry years (76%-95%) was greater than that of wet years (64%-86%). We also found that sub-permafrost groundwater flows increased significantly with permafrost degradation. Sub -permafrost groundwater flows increased more rapidly than that of supra-permafrost groundwater flows over the past decades. Future climate change may further affect runoff composition in permafrost rivers; and our method has great potential to characterize it.