In this work, a smart cure cycle with cooling, polymerization and reheating was devised to nearly completely eliminate thermal residual stresses in the bonding layer of the co-cure bonded hybrid structure. In situ dielectrometry cure monitoring, DSC experiments and rheometric measurements were performed to investigate the physical state and the cure kinetics of the neat epoxy resin in the carbon fiber/epoxy composite materials. From the experimental results, an optimal cooling point in the cure cycle was obtained. Also, process parameters such as cooling rate, polymerization temperature and polymerization time in the curing process were investigated. Then, the thermal residual stresses were estimated by measuring the curvatures of co-cure bonded steel/composite strips and their effects on the static lap-shear strengths of co-cure bonded steel/composite lap joints were measured. Also, the effects of thermal residual stresses on the tensile strength, the interlaminar shear strength and the interlaminar fracture toughness of the composite material itself were measured using tensile, short beam shear and double cantilever beam tests. From these results, it was found that the smart cure cycle with cooling, polymerization and reheating eliminated the thermal residual stresses completely and improved the interfacial strength of the co-cure bonded hybrid structures, as well as the tensile strength of the composite structures.