Needle-punching is used as an alternative to expensive and sophisticated three-dimensional (3D) weaving processes to prepare a 3D composite. In this study, a 3D needled carbon–carbon (C/C) composite structure was examined using X-ray tomography and scanning electron microscopy (SEM). The effects of manufacturing porosities, needling diameter and needling density on the thermal conductivity of the composite were determined through multiscale finite-element modelling. The degradation of thermal conductivity caused by the manufacturing porosity was higher in the longitudinal direction than in the through-thickness direction. Moreover, it was found that the through-thickness thermal conductivity of the composites increased with increasing needling diameter and density.