The combination of honeycomb structure and carbon/carbon (C/C) composites offers unique high load-bearing and light-weight advantages in satellite-bearing platforms. However, the defects generated by the imperfect preparation process are inevitable. This paper employs the chemical vapor infiltration (CVI) technique to fabricate novel C/C honeycomb structures and considers the presence of internal void defects. Based on micro-computerized tomography (μ-CT) images, the void distribution and porosity as well as the micro-structure characteristics are acquired. Meso-scale representative volume element (RVE) models is established to predict the performance of honeycomb wall material. A secondary development of ABAQUS is performed to establish a model of honeycomb structure containing void defects. Multi-scale models are developed for investigating the mechanical performance of the C/C honeycomb structure. Experimental methods and finite element simulations are utilized to examine the effects of porosity and different weave structures on the compression and shear properties, as well as damage modes of C/C honeycomb structures in detail. The results demonstrate that the presence of low porosity ρ = 1 % severely diminishes the load-bearing capacity of the honeycomb and affects its damage pattern. Twill-2 weave C/C honeycomb inherits the advanced performance of the composites and exhibits superior comprehensive properties compared to plain weave and twill-1 weave honeycomb structures.