Three-dimensional fabric composites have evolved as an attractive structural material for multi-directional load bearing and impact application. However, research on prediction of their behavior before being fabricated is inadequate. This article reports a two-step modeling approach for predicting the effective mechanical properties of three-dimensional fabric carbon fiber-reinforced composites. In step one, the micro-heterostructural composites were represented by microscale cylindrical, square, or hexagonal prismatic representative volume elements, containing a long carbon fiber surrounded by polymer matrix, taking into account the transversely isotropic properties of carbon fibers. The mechanical properties of each representative volume element were extracted from the modeling results of uniaxial tensile, lateral expansion, and transverse shear tests, using appropriately derived formulae, and averaged as the equivalent mechanical properties of the micro-heterostructures. In step two, a three-dimensional fabric composite unit cell was represented by a three-dimensional finite element model, taking into account the fiber orientations and fabric architecture. A three-dimensional orthogonal fabric carbon fiber-reinforced epoxy composite was selected as the case study material. The overall orthotropic mechanical properties of the composites were predicted by conducting tensile and shear tests on the unit cell. The modeling results show that the Young’s moduli in fiber oriented directions and shear moduli are significantly higher than those of the matrix. The shear moduli of shearing fiber cross-sections are even much higher than that of shearing along fiber longitudinal direction. Carbon fiber can improve structural stability by lowering the Poisson’s ratios of the composites. The modeling results were compared with and validated by the experimental tests.