In this study, we investigated the room-temperature wafer bonding of indium phosphide (InP) and its atomic-scale bond interface formation. The direct bonding of InP/InP wafers via surface-activated bonding (SAB) and room-temperature bonding involving an activated Si atomic layer was compared. Particularly, the bond strength, surface morphology, and atomic structure in the bond interface were investigated. In contrast to SAB, the bonding involving the activated Si atomic layer afforded more than 2-fold increase in bond strength. This is because, unlike that in SAB, the InP surface was not directly irradiated by an Ar fast atomic beam; instead, a layer of activated Si atoms was deposited. Consequently, the surface roughness of the wafers was lower than that obtained using SAB. The atomic structure of the wafer surface was maintained after activation, and atomic contact between the wafers was achieved. The diffusion of In and P into the Si atomic layers affected the bond strength, indicating that the InP-InP bonding in the wafers through an activated Si atomic layer was different from the simple bonding of two Si bulks. Notably, the state of the bond interface obtained via SAB was different from that obtained via SAB of other semiconductor materials. The room-temperature bonding method will be significantly useful in the development of fabrication techniques for the heterogeneous integration of InP-based electronics and photonics.