In this paper, the virtual material characterization of three dimensional (3D) orthogonal woven composite materials is investigated by large-scale finite element analyses to predict the elastic properties. To numerically model the complex geometry of 3D orthogonal woven composites, a unit structure including the stuffer yarns, filler yarns, weaver yarns, and the resin region is generated based on direct numerical simulation (DNS) and the unit structures with the same pattern are assembled into an orthogonal woven composite structure composed of several millions of degrees of freedom. The influence of the geometrical irregularities, such as the inconsistent tow spacing and the waviness of the filler yarn, on the mechanical properties are also discussed by separately generating the yarns and the resin. From the numerical examples, it is shown that the pattern of tow distribution affects the shear modulus, and the direct modeling of the wavy yarns can produce more accurate stiffness knockdown. It is also emphasized that large-scale numerical analyses can be one of the methodologies sufficient for the material characterization of the orthogonal woven composites and can be more applicable in the realistic structure subject to complex loading compared to the unit cell approach.