Abstract Investigations of the thermal conductivity of thermally damaged Beishan granite under uniaxial compression were conducted. Rectangular prism specimens preconditioned at 105 °C were heated at different temperatures (400, 550 and 650 °C) and then cooled to room temperature (27 °C) for testing. Using the transient plane source (TPS) method, in combination with a servo-controlled compression machine and an acoustic emission (AE) monitoring system, lateral thermal conductivities, stress–strain relations and AE responses of the thermally treated specimens during uniaxial compression were measured. The effects of thermal treatment temperature on the strength, deformation and AE parameters were analyzed. The lateral thermal conductivity evolution characteristics for the specimens in the deformation process were studied. The stress-and-deformation-dependent lateral thermal conductivities were also evaluated. The experimental results indicate that the lateral thermal conductivity varies nonlinearly with increasing axial stress due to closure, initiation and propagation of microcracks within the specimens. Moreover, significant differences exist in the lateral thermal conductivity behaviors between the specimens subjected to different temperature treatments. Furthermore, to reveal the influence of cracking behaviors on the thermal conductivity of the thermally damaged specimens in compression, numerical modeling was performed using PFC and the simulation results agree well with the experimental data.