Wafer bonding apparatus and method are provided. A method includes performing a first plasma activation process on a first surface of a first wafer. The first plasma activation process forms a first high-activation region and a first low-activation region on the first surface of the first wafer. A first cleaning process is performed on the first surface of the first wafer. The first cleaning process forms a first plurality of silanol groups in the first high-activation region and the first low-activation region. The first high-activation region includes more silanol groups than the first low-activation region. The first wafer is bonded to a second wafer.