The natural fracture system exerts a significant influence on the physical and mechanical properties of rock masses. The heat transfer in fractured rock masses is much more complicated than that of intact rock due to the thermal contact resistance induced by natural fractures with varying size, aperture, roughness, and orientation. This work describes a method for determining the representative element volume (REV) of heat transfer and the 3D thermal conductivity tensor of fractured rock masses. The method is based on the element-wise averaging of temperature and heat flux, which can be obtained from a finite element solution to a steady state heat transfer problem with specific boundary conditions. A case study was conducted based on the geological data of a potential area for high level radioactive waste disposal in China. The results indicate that the size of heat transfer REV of the rock masses in the study area is approximately 18 m × 18 m × 18 m. 3D thermal conductivity tensor, the magnitudes and directions of the three principal thermal conductivities, and anisotropy of the fractured rock masses were obtained. Influences of main fracture parameters including density, disc diameter, and thermal contact resistance on the heat transfer characteristics were investigated. The research results in this work can provide a better understanding of the discontinuous heat transfer processes in fractured rock masses and their homogenization methods.