A real microstructure-based finite element model of 3D-hybrid carbon/carbon (3DH C/C) composite is used for the prediction of effective thermal expansion coefficient over the full temperature range (27–2227 °C). The representative volume elements of the real microstructure of 3DH C/C composite include the realistic features such as cross-sectional distortions of the bundle and irregularly shaped voids. Two-scale homogenization approach has been utilized to determine the effective thermomechanical behavior of the composite. The effective elastic properties of the fiber bundles are firstly obtained using the mean-field homogenization approach also called the Mori–Tanaka approach. Later, the computational homogenization approach is utilized for the prediction of effective coefficients of thermal expansion (CTEs) of bundles and 3DH C/C composite. The effective CTEs obtained for 3DH C/C composite are found in good agreement with those obtained through experiments in the literature.