Global warming has aggravated the problem of permafrost degradation, the long-term variation of which is not well estimated. In this study, a fully coupled hydrothermal dynamics cold region hydrologic model was used to quantify the historical spatial–temporal characteristics of permafrost degradation by estimating the depth to permafrost table (DPT), taliks in different subbasins, maximum frozen depth (MFD) for seasonally frozen ground (SFG), thaw date (TD), and annual number of frozen days (NFD) in the headwaters of the Yellow River (HWYR) in eastern High Mountain Asia. The model considered the taliks and successfully estimated four historical fine-scale permafrost maps. Permafrost degradation began with the enlargement of active layer thickness (ALT), formation of taliks, rise in the permafrost bottom, and merging of the permafrost table and bottom, and ended with a decrease in MFD. From 1980 to 2014, the permafrost area (PA) in the study area decreased by a total of 17,849 km2 at a rate of more than −7100 km2/decade (−5.8 %/decade). The mean DPT increased by 0.8 m at 31.76 cm/decade and more than 100 cm/decade at the grid scale. The absolute MFD (AMFD) decreased by 0.11 m at −14.47 cm/decade. The mean TD decreased by 14.28 days at −5.56 days/decade and more than −20 days/decade at the grid scale. The mean NFD decreased by 25.51 days at −9.97 days/decade. The lowland area had a smaller NFD and an earlier TD than the mountainous area. Basins with a large air temperature (AT) and small elevation had a small DPT, MFD, TD, NFD, a large rate of decrease in TD and NFD, and increase in absolute DPT (ADPT), and a small rate of decrease in AMFD. The rates of increase in ADPT and decrease in AMFD were close to 0 when the change in AT was lower than 0.55 °C/decade.