This work presents experimental and numerical investigations of three-dimensional (3D) fiber orientation on mechanical impact behavior of short glass-fiber-reinforced polyether ether ketone (SGFR PEEK) composites. The incorporation of short fibers significantly enhances the stiffness and strength of the composites while reducing the ductility, thereby, making the study of their impact response essential. To this end, we firstly manufactured the composite components using injection molding, and used the micro-computed tomography (µCT) to measure the fiber orientation distribution in 3D space for mechanical behavior prediction. Then, by studying the molded components across the thickness based on the actual observation, a distinct laminate structure with seven layers was quantitatively evaluated. A representative volume element (RVE) micromechanical computational method was developed and compared with the experimental results. Furthermore, homogenization method with the periodic boundary condition was implemented to evaluate the effective mechanical properties of the molded components. Finally, the phenomenological Johnson Cook (JC) model with fracture behavior was conducted to analyze the impact response of the injected components with different fiber orientation distributions. The new framework is demonstrated by acceptable energy absorption capability prediction of the SGFR PEEK composites.