The characterization of thermal transport in fractured rocks is crucial for understanding numerous systems of environmental, geological and industrial importance. Fracture wall roughness exhibits long range spatial correlations and induces a heterogeneous aperture field, thus promoting the formation of preferential flow channels within fracture planes. Here, we develop a modelling approach to identify geometrical parameters of individual fractures that control the heat exchange at the fluid/rock interface and the advection of heat along the fracture.