This paper presents the synthesis, characterization, and multiscale modeling of hybrid composites with enhanced interfacial properties consisting of aligned zinc oxide (ZnO) nanowires and continuous carbon fibers. The atomic layer deposition method was employed to uniformly synthesize nanoscale ZnO seeds on carbon fibers. Vertically aligned ZnO nanowires were grown from the deposited nanoscale seeds using the low-temperature hydrothermal method. Morphology and chemical compositions of ZnO nanowires were characterized to evaluate the quality of synthesized ZnO nanowires in hybrid fiber-reinforced composites. Single fiber fragmentation tests reveal that the interfacial shear strength (IFSS) in epoxy composites improved by 286%. Additionally, a multiscale modeling framework was developed to investigate the IFSS of hybrid composites with radially aligned ZnO nanowires. The cohesive zone model (CZM) was implemented to model the interface between fiber and matrix. The damage behavior of fiber was simulated using the ABAQUS user subroutine to define a material’s mechanical behavior (UMAT). Both experimental and analytical results indicate that the hierarchical carbon fibers enhanced by aligned ZnO nanowires are effective in improving the key mechanical properties of hybrid fiber-reinforced composites.