Adhesive joining and Z-pinning techniques are commonly used in assembling aerospace composite parts, such as ailerons, spars, ribs, and tails. The current study reports a novel dual-scale approach to synergistically toughen the co-bonded joints (CBJs) by simultaneously loading carbon nanotubes (CNTs) and Z-pins. Shear results depict that combining CNTs and Z-pins creates a synergistic effect owing to inherent and extraneous toughening mechanisms. The results showed that combining CNTs and Z-pins endorses maximum shear strength under tensile loading with a 119.7% improvement compared to unmodified CBJs. The investigation on failure surfaces demonstrates that the dual-strengthening approach changes the sudden failure of CBJs to a steady mode owing to synergistic effects, which include rough assembly region, shear band, crack path variation, and effective linking of Z-pins. Furthermore, a vibration analysis shows that dually reinforced CBJs had higher natural frequencies than other samples. The artificial neural network (ANN) model precisely predicted the failure load with an acceptable margin of error. The results from the ANN, with R 2 values of 0.99507 for training and 0.99492 for the overall model, fall within the permissible error range, indicating that the experimental and ANN outcomes are consistent.