<p>Accurately assessing the heat transfer characteristics of the repository’s barrier system and precisely predicting the evolution of the temperature field over the entire lifecycle of the repository are of vital importance for its design and safe operation. In this paper, a novel method for determining the thermal contact resistance (TCR) at the bentonite and granite interface is presented. This approach is grounded in steady state heat transfer experiments and finite element numerical simulations. The novel method effectively avoids measurement errors caused by inaccuracies in the positioning of pre-drilled temperature measurement holes. Based on the developed method, the impact of factors including the dry density of compacted bentonite, the type of bentonite additives, normal stress, and interface roughness on the contact heat transfer characteristics at the bentonite–granite interface is further explored. It is found that the TCR decreases with the increasing dry density of bentonite, and the decreasing trend exhibits an initial rapid decline, followed by a slower reduction, and eventually stabilizes. Additive utilization can effectively mitigate the TCR. Under the same additive proportion, graphite exerts the most pronounced impact on reducing the TCR, followed by quartz, and granite powder has the least effect. As the JRC value of the contact surface rises, the overall TCR also increases. For a contact interface with a given roughness, the TCR diminishes as the normal stress increases.</p>