Cu–Cu joints have been adopted for ultra-high-density packaging for high-end devices. However, the atomic diffusion rate is notably low at the preferred processing temperature, resulting in clear and distinct weak bonding interfaces, which, in turn, lead to reliability issues. In this study, a new method for eliminating the bonding interfaces using two types of Cu films in Cu–Cu bonding is proposed. The difference in grain size was utilized as the primary driving force for the migration of bonding interfaces/interfacial grain boundaries. Additionally, the columnar nanotwinned Cu structure acted as a secondary driving force, making the migration more significant. When bonded at 300 °C, the grains from one side grew and extended to the bottom, eliminating the bonding interfaces. A mechanism for the evolution of the Cu bonding interfaces/interfacial grain boundaries is proposed.