AbstractSupra‐ and sub‐permafrost groundwater are the two main components of groundwater in permafrost regions. However, due to the lack of groundwater observational data, the spatial‐temporal differentiation of these groundwater components in permafrost basins remains unclear. Based on flow data from 17 hydrological stations in five permafrost rivers within the Eurasian Arctic and Qinghai‐Tibet Plateau permafrost regions, this study tries to determine the proportion of supra‐ and sub‐permafrost groundwater through the corresponding relationship between baseflow separation and baseflow index. The results showed that the annual average contribution of supra‐ and sub‐permafrost groundwater in river runoff to total streamflow in the Yangtze River source basin was 36.81% and 14.56%, respectively. Correspondingly, the Yellow River source basin was 36.58% and 24.46%, the Ob River basin was 37.05% and 26.83%, the Yenisei River basin was 28.80% and 36.56%, and the Lena River basin was 39.13% and 9.54%. Over the past 50–80 years, the ratio of sub‐permafrost groundwater discharge to river runoff and the flux of sub‐permafrost groundwater have shown an increasing trend in all study basins, which was significantly affected by air temperature and permafrost area. Relative contribution of supra‐permafrost groundwater exhibits a significant positive correlation with precipitation and permafrost area. Air temperature has both positive and negative effects on supra‐permafrost groundwater discharge, leading to a rising or falling trend of supra‐permafrost groundwater discharge. In the future, it is necessary to further explore the complex effects of groundwater discharge variations on streamflow in permafrost regions under climate warming.