A micro-structurally informed two scale unit cell analysis has been presented for the prediction of thermal conductivities of 3D hybrid and 4D in-plane carbon/carbon composites. Realistic micro-structural features such as bundle cross sections, alignments, and macro voids have been included directly in the unit cells geometry through reconstructed X-ray computed tomography images of the composite. Asymptotic homogenization technique has been used on both scales (bundle and composite) along with periodic boundary conditions to obtain effective thermal conductivities. The imperfectly bonded conditions at the fiber/matrix and fiber bundle/matrix interfaces have also been modeled by considering the contact and equivalent gap conductance between their surfaces. The model has been validated through the experiment conducted in the in-plane direction of 3D hybrid composite. Finally, the effective thermal conductivities of 3D hybrid composite in out-of-plane directions and of 4D in-plane composite in x, y, and z-directions have been predicted for full temperature range (300–1500 K).