A microstructure-sensitive thermomechanical simulation framework is developed to predict the mechanical and heat transfer properties of vertically aligned CNT (VACNT) arrays used as thermal interface materials (TIMs). The model addresses the gap between atomistic thermal transport simulations of individual CNTs (carbon nanotubes) and experimental measurements of thermal resistance of CNT arrays at mesoscopic length scales. Energy minimization is performed using a bead–spring coarse-grain model to obtain the microstructure of the CNT array as a function of the applied load. The microstructures obtained from the coarse-grain simulations are used as inputs to a finite volume solver that solves one-dimensional and three-dimensional Fourier heat conduction in the CNTs and filler matrix, respectively. Predictions from the finite volume solver are fitted to experimental data on the total thermal resistance of CNT arrays to obtain an individual CNT thermal conductivity of 12 W m^{−1} K^{−1} and CNT–substrate contact conductance of 7 × 10^{7 }W m^{−2} K^{−1}. The results also indicate that the thermal resistance of the CNT array shows a weak dependence on the CNT–CNT contact resistance. Embedding the CNT array in wax is found to reduce the total thermal resistance of the array by almost 50%, and the pressure dependence of thermal resistance nearly vanishes when a matrix material is introduced. Detailed microstructural information such as the topology of CNT–substrate contacts and the pressure dependence of CNT–opposing substrate contact area are also reported.