High-density electronics are hindered by the constraints of Sn-based solder joints, necessitating the exploration of Cu–Cu solid-state bonding. However, current bonding methods are expensive and time-consuming; therefore, understanding the Cu–Cu bonding mechanism is crucial for optimization. This study utilizes molecular dynamics (MD) simulation to elucidate the Cu–Cu solid-state bonding behavior, focusing on interfacial densification and diffusion phenomena. Furthermore, it highlights the influence of crystal orientation on the interfacial bonding behavior. To analyze the impact of crystal orientation, monocrystalline Cu slabs with a simplified periodic surface structure were employed to replicate surface roughness and subsequently bonded at a specific temperature. The results indicate the critical influence of crystalline orientations on the bonding process: identical orientations result in slower densification at the interface, whereas misoriented orientations significantly accelerate it. This effect, attributed to the grain boundary (GB) structures formed owing to misorientation, suggests a central role for GB diffusion in bonding progression. Diffusion coefficients calculated using the mean square displacement (MSD) confirmed these findings and exhibited significantly larger values for misoriented joints. Additionally, the simulations reveal an activation energy for GB diffusion that is lower than conventional values, highlighting the impact of the crystallographic orientation and voids at the bonding interface. Our research elucidates the role of crystalline orientation in diffusion phenomena at bonding interfaces, offering valuable implications for optimizing bonding-based manufacturing processes.