This study aimed to quantify the 3D microstructure of short basalt fiber (BF)-reinforced polyamide 6,6 (PA6,6) composites, in an attempt to more accurately predict their mechanical properties. Thermoplastics are often reinforced with short fibers to improve their strength. BF is a natural fibrous material and a potential option for thermoplastic reinforcement. However, injection-molded composite materials, including thermoplastics, have microstructural properties that evolve during the molding process. Thus, a method for quantifying the microstructure of short fiber-reinforced plastic (SFRP) composites is of particular interest with regard to predicting and optimizing the performance thereof. In this study, nondestructive analysis of the internal microstructure of injection-molded, SBF/PA6,6 composites was conducted using micro-computed tomography (μ-CT) imaging. All of the composite components, including the SBFs, PA6,6, and voids, were reconstructed into 3D digital images and subsequently defined as basic structural models. To investigate the effects of fiber length and orientation on the mechanical properties of the composites, longitudinally and transversely fiber-oriented SBF/PA6,6 composite specimens were carefully compared. μ-CT-assisted analytical measurements were then conducted using the reconstruction models and simulation tools to determine the fiber length, orientation distribution, and anisotropic mechanical properties. The resulting microstructure-based predictions yielded valuable information clarifying the relationship between the 3D microstructure and mechanical properties of injection-molded SBF/PA6,6 composites. The results showed a 20% increase in the tensile strength of specimens having SBFs oriented in the longitudinal versus transverse direction. Thus, the anisotropic nature of the composites, attributable to the internally dispersed fibers, has an effect on the composite's mechanical properties. This article provides an important overview of predictive technologies based on the internal microstructure of SFRPs, and insight into the means to further advance this technology.