The design of heterojunction devices is typically limited by material integration constraints and the energy band alignment. Wafer bonding can be used to integrate material pairs that cannot be epitaxially grown together due to large lattice mismatch. Control of the energy band alignment can be provided by formation of interface dipoles through control of the surface chemistry. We have developed an ultra-high-vacuum system for wafer-fusion-bonding semiconductors with in situ control and measurement of surface properties relevant to interface dipoles. A wafer-fusion-bonding chamber with annealing capabilities was integrated into an ultra-high-vacuum system with a sputtering chamber and an x-ray photoelectron spectroscopy system for preparing and measuring the surface chemistry of wafers prior to bonding. The design of the system along with initial results for the fusion-bonded InGaAs/Si heterojunction is presented.