In recent years, degradation of perennial permafrost has occurred against the background of a clear warming trend. Therefore, it is of great scientific significance to carry out research on permafrost changes and hydrological response under multi-year climate change conditions. Taking the Irtysh River Basin as the study area, this paper explores the connection between perennial permafrost changes and climate by taking multi-year meteorological data as the support and adopting SHAWDHM, a distributed hydrological model coupled with a permafrost module, to simulate the upstream sub-watersheds of the headwater area of the Irtysh River Basin. At the same time, we analyzed the permafrost hydrological change pattern of the upper watershed of the Irtysh River basin from 1968 to 2022, and simulated the year-by-year changes of soil infiltration, measured 20% annual precipitation, and the proportional relationship of the area of perennial permafrost to the total area of the watershed. The planar distribution of perennial permafrost degraded significantly from 1990 to 2022, and the newly added and degraded permafrost were located in the area where seasonal permafrost was in transition to perennial permafrost. The proportion of perennial permafrost area fluctuates above and below 35% from 1972 to 1996, and the change of soil infiltration obtained by simulation is mainly affected by the change of precipitation. And after 2008, with the increase of temperature, the soil hydraulic conductivity increases, and the soil infiltration volume rises rapidly when the increase of precipitation is not significant.