Wafer bonding technology is one of the key processes for high density and high performance semiconductor devices. However, bonding pads could not be directly observed with visible light after wafer bonding because of the thick silicon substrate. In this paper, we demonstrated high-precision bonding overlay control techniques using a bonding machine, an advanced process control (APC) system, and a newly developed overlay measurement tool that uses infrared (IR) light. The accuracy of the IR-light overlay measurement was verified by using a conventional visible-light tool after back-side silicon removal. The verification results showed good measurement repeatability and accuracy of the IR-light measurement which can be performed right after wafer bonding.