This work presents a technique to estimate the spatially varying thermal contact conductance (TCC) over the contact zone of non-conformal bolted joints, which are common in satellite structures for mounting of the electronic packages, through a coupled thermal and structural analysis. The heat flow across an interface occurs only through the actual regions of contact rather than the apparent contact area and is governed by the TCC at the interface. Due to its multi scale nature, accurate estimation of TCC is very challenging. In this work, the TCC between two plates, which are joined using a single bolt at the center is determined for four prescribed bolt torques viz. 1.5, 3.0, 4.5 and 6.0 Nm, using non-intrusive temperature measurements performed at locations away from the actual interface. TCC depends upon micro contact conductance of surface asperities and also on the macroscopic deflection of plates occurring due to the application of bolt torque. The effect of micro contact conductance due to surface asperities are modelled by making the TCC a linear function of applied torque. The macroscopic deformation of plates are found by solving the three dimensional state of stress using finite element analysis. The slope parameter connecting TCC and contact pressure is estimated for each torque, for a specified heat flux and sink temperature, via an inverse technique by minimizing the difference between the simulated temperature obtained by the assumed value of slope parameter and the one obtained from the experiments in a least square sense. Subsequently, the estimated values of the TCC are validated by comparing the simulated temperatures with the measured ones obtained from the experiments performed at different conditions (heat fluxes and sink temperatures) for each bolt torque. As the bolt torque increases, due to the deformation of the asperities, the actual contact area increases and approaches the macroscopic contact area. Consequently, the TCC increases and tends to reach a saturation value. This is also manifested by the estimated slope parameter approaching a constant value asymptotically as the bolt torques are increased. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023.