This paper presents an efficient multiscale approach for high fidelity virtual testing of highly aligned short fiber reinforced composites (SFRCs), based solely on constituent material and interface properties with no need of calibration data. The method is based on a hierarchical, bottom-up characterization of SFRCs and the link of mechanical behaviors of materials and microstructures from a lower scale to a higher scale. It starts with a microscopic unit cell model to estimate the transverse and shear properties of the aligned short fiber composites. Next, two types of mesoscale models with explicit consideration of fiber discontinuity and possible local fiber misalignments are employed to obtain effective properties of material domains with such morphologies. Such obtained meso-scale mechanical properties and damage behaviors are then integrated into the macroscale virtual laminar via the stochastically integrating of possible material defects. Results indicate that for perfectly aligned SFRCs the strength reduction is about 25% as compared to that of the continuously reinforced composites. However, misalignment of short fibers can cause a further strength reduction of 20–35% with the volume fraction of the misalign regions varying from 1% to 10%.