With the miniaturization and high integration of electronic devices, high-performance thermally conductive composites have received increasing attention. The construction of hierarchical structures is an effective strategy to reduce interfacial thermal resistance and enhance composite thermal conductivity. In this study, by decorating carbon fibers (CF) with needle-like ZnO nanowires, hierarchical hybrid fillers (CF@ZnO) were rationally designed and synthesized using the hydrothermal method, which was further used to construct oriented aligned filler networks via the simple freeze-casting process. Subsequently, epoxy (EP)-based composites were prepared using the vacuum impregnation method. Compared with the pure CF, the CF@ZnO hybrid fillers led to a significant increase in thermal conductivity, which was mainly due to the fact that the ZnO nanowires could act as bridging links between CF to increase more thermally conductive pathways, which in turn reduced interfacial thermal resistance. In addition, the introduction of CF@ZnO fillers was also beneficial in improving the thermal stability of the EP-based composites, which was favorable for practical thermal management applications.