Drilling into subglacial lakes in the polar regions is of great significance for reconstructing the evolution of ice sheets, understanding ice dynamics, and exploring unknown life forms. Currently, China is planning to carry out a scientific drilling project at Qilin Subglacial Lake in the near future. To enable clearly drilling and sampling of the Qilin Subglacial Lake, a new drilling method that combines a hot water drill with a RECAS was proposed. It was also proposed to use both the natural freezing and the active cooling methods to isolate the borehole drilled by the hot water drill and the RECAS. To evaluate the applicability of these two methods for the Qilin Subglacial Lake drilling project, the temperature distribution within the overlying ice sheet was first simulated. Subsequently, numerical models of the two aforementioned methods were developed using COMSOL Multiphysics 5.6 software. Subsequently, the borehole freezing time was estimated for both methods through numerical simulation. For the natural freezing method, the safe drilling distance and safe drilling time for the RECAS operation were calculated. Meanwhile, the required cooling power density was determined for the active cooling method. Furthermore, the feasibility of the two methods was compared and evaluated. The results indicate that the active cooling method should be prioritized for separating the hole drilled by hot water and RECAS in the actual drilling project at Qilin Subglacial Lake. The power density of cooling is suggested to be controlled at about 0.19 W/cm². Under these conditions, the hot water borehole can be completely frozen within 8 h.