This study proposes a novel algorithm for generating representative volume elements which mitigate microstructural inhomogeneities in fiber-reinforced composites. The algorithm integrates void characteristics obtained from micro-computed tomography to more accurate microstructure models. Based on these models, the effects of void content, spatial distribution, and void diameter on the mechanical behavior of CF/PEEK composites are systematically evaluated using finite element analysis and experimental validation. The results reveal that void content significantly reduces transverse tensile strength and ductility, while void size further accelerates failure and enhances brittleness. In contrast, void distribution has minimal influence on the transverse mechanical response. These findings not only offer qualitative insights into void-induced damage mechanisms but also provide a theoretical basis for optimizing microstructures to enhance the mechanical performance of CF/PEEK and similar composite systems. Finally, the limitations of this study have been discussed, and directions for future research are proposed.