Abstract: The supra-permafrost water is a vital water source to support the ecosystem and an important link in maintaining the hydrothermal cycle in the permafrost area. Under the intensification of climate change, scientific understanding of the effect of permafrost degradation on the supra-permafrost water is of great significance to water resources and ecological protection. Focusing on the hydrological effects of permafrost degradation in the source areas of the Yellow River, this study analyzed the degradation characteristics of permafrost, and revealed the response of the depth of groundwater level and recharge process of the supra-permafrost water to the permafrost degradation, on the basis of the temperature and moisture content of frozen soil at typical monitoring points and the runoff change at the Huangheyan Hydrologic Station. The results show that the average temperature increased 0.42 °C at the 0−2.4 m profile of the monitoring point from 2010 to 2020. The depth of the upper interface of the permafrost reduced from 2.1m to 2.5 m, with an average decrease rate of 4cm/a. After 2018, the depth of supra-permafrost water level reduced from less than 0.9 m to 0.9−1.8 m. The permafros degradation led to the runoff process in the melting period of active layer (May−October) being advanced, the ratio of extreme value being reduced, and the runoff hydrograph in January being more prominent. Ground temperature is the dominant factor in controlling the changes of depth of the supra-permafrost water. Under the condition of warm and humid climate change, Permafrost degradation would change the dynamic characteristics of the water above the frozen layer and its hydraulic relationship with surface water, affecting the hydrological and ecological processes in the source area of the Yellow River.