The effect of bonding duration and substrate temperature on the nano-scale interfacial structure for bonding strength were investigated using high resolution transmission electron microscopy. It shows that intermetallic compound crystallization correlates with bonding duration, as a longer duration is applied, alumina fragmentation becomes pervasive, resulting in continuous alloy interfaces and robust bonds. In addition, a substrate temperature (i.e. 175 °C) promotes the fracture of alumina, and simultaneously contributes to the interfacial temperature, accelerating interdiffusion and facilitating the formation of intermetallic compounds, therefore increasing bonding strength. The compound formed during bonding is CuAl2, regardless of the bonding parameters applied.