Thermokarst lakes in the Qinghai–Tibet Plateau (QTP) are increasing in number and lake surface area, intensifying the lake–permafrost interaction and making it more complex, thus affecting the hydrological and ecological environment. Although the impact of the individual lake on permafrost has been studied, the effects of lakes group on permafrost and regional hydrological processes remain unexplored. Hence, in this study, modified SUTRA models considering thermal conduction and convection processes were established for five scenarios, including a current environment and four thought experiments, to determine whether and how thermokarst lakes group accelerates permafrost degradation. The models could effectively simulate the variations in the ground temperature with time and depth, with the highest RMSE and lowest R2 being 1.443 °C and 0.706, respectively. Thermal conduction and convection played a dominant role before and after the formation of through-taliks below the thermokarst lakes, respectively. Through-taliks strengthened the hydraulic connection between supra-permafrost water, sub-permafrost water, and lakes, and changed the groundwater circulation pattern. An increase in the number of thermokarst lakes led to the formation of more through-taliks and improved the heat transfer efficiency, accelerating permafrost degradation. Thermal erosion of the permafrost base was more severe in the presence of a recharge source and pathway via a talik. The results highlight the importance of thermal convection and groundwater circulation in permafrost degradation. The findings can help understand the interaction mechanism between permafrost and thermokarst lakes and the variation in environmental and eco-hydrological processes in cold regions.