Embodiments of mechanisms for cleaning a surface of a semiconductor wafer for a hybrid bonding are provided. The method for cleaning a surface of a semiconductor wafer for a hybrid bonding includes providing a semiconductor wafer, and the semiconductor wafer has a conductive pad embedded in an insulating layer. The method also includes performing a plasma process to a surface of the semiconductor wafer, and metal oxide is formed on a surface of the conductive structure. The method further includes performing a cleaning process using a cleaning solution to perform a reduction reaction with the metal oxide, such that metal-hydrogen bonds are formed on the surface of the conductive structure. The method further includes transferring the semiconductor wafer to a bonding chamber under vacuum for hybrid bonding. Embodiments of mechanisms for a hybrid bonding and a integrated system are also provided.