River flow characteristics in permafrost regions on the Qinghai-Tibet Plateau (QTP) have changed rapidly with the intensification of global warming. However, the specific change characteristics and their responses to changes in influencing factors remain unclear. Based on the multi-year flow data of several typical basins in the QTP permafrost regions, combined with the flow duration curve and percentile flow, this study analyzed the variability of annual peak discharge, Q5, Q10, and Q30 (5%, 10%, and 30% percentile flows in the flow duration curve, respectively) and their response relationships with different climate change factors. In addition, the corresponding relationships between different percentile high flows and annual hydrographs were analyzed. The results indicate that, in the context of global warming, changes in the high flows in permafrost regions are bidirectional, either rising or falling, or both. Moreover, the responses of different percentile high flows to climate change are seasonally distinct. Spring high flows are more sensitive to changes in air temperature and normalized difference vegetation index (NDVI), and summer and autumn high flows are more susceptible to corresponding changes in seasonal average precipitation and rainfall intensity. In addition, different percentile high flows can be used to predetermine the level of annual flood events. Among them, the largest, the larger, and all other general flood events during the annual flood season, can be defined by Q5, Q10, and Q30, respectively. The analysis of different high flows combined with the flow duration curve is essential for the further clarifi-cation of the hydrological processes in permafrost regions. The prudent utilization of water resources benefits the sustainable development of human society.