A method of semiconductor wafer bonding and system thereof are proposed. A first alignment mark of a first semiconductor wafer is aligned with a second alignment mark of a second semiconductor wafer. A partial attachment is performed between the first semiconductor wafer and the second semiconductor wafer. A scanning is performed along a direction substantially parallel to a surface of the first semiconductor wafer. It is determined if a bonding defect of the partially attached first semiconductor wafer and the second semiconductor wafer exists.