With the recent demand for weight reduction, structural materials for transportation equipment are being replaced by carbon-fiber-reinforced thermoplastics (CFRTPs). Therefore, techniques to join CFRTPs to alloys are needed. In this study, the fatigue delamination growth of bonded CFRTP/aluminum alloy joints was characterized. The specimens were bonded in three ways, using adhesive, direct chemical bonding, and direct chemical bonding with a nanostructured surface. The type of the specimen was double cantilever beam (DCB) specimen, which consisted of aluminum alloy (A5052) and plain woven CFRTP. The lay-up of the CFRTP was [(0,90)]9 and the used matrix was PA6. Fatigue loading was applied in displacement control mode. The ratio between the minimum and maximum displacement was 0.1, and the test frequency was 5 Hz. The crack length during the fatigue tests was obtained by compliance calibration. Fatigue was characterized by constructing a Paris diagram for each specimen type. The fracture surface distinctively changed from smooth brittle-like fracture to hair-like ductile fracture post fabricating a nanostructure and chemical bonding. As a result, the fatigue crack growth resistance of the specimen with the nanostructure significantly improved due to the hair-like ductile fracture.