Electrical performance was found to be closely related to the variation of nanosized interface morphology. This work investigated in detail the microstructural development of in- and anti-phase bonded interfaces for n-type (100) GaAs wafers treated at 500, 600, 700 and 850 °C. The interfacial energy of anti-phase bonding is higher than that of in-phase bonding based on the first-principles calculations. The higher interface energy tends to stabilize the interfacial oxide layer. The continuous interfacial oxide layer observed below 700 °C behaves to deteriorate the electrical property due to its insulating property. However, the existence of nanoscaled oxide at anti-phase bonded interfaces can improve the electrical conductivity at 700 °C. The reason will be discussed based on the analysis of autocorrelation function from HRTEM (high-resolution transmission electron microscope) and energy dispersive x-ray spectroscopy.