The present invention relates to a wafer cleaning and a wafer bonding method using the same that can improve a yield of cleaning process and bonding property in bonding the cleaned wafer by cleaning the wafer using atmospheric pressure plasma and cleaning solution. The wafer cleaning method includes the steps of providing a process chamber with a wafer whose bonding surface faces upward, cleaning and surface-treating the bonding surface of the wafer by supplying atmospheric pressure plasma and a cleaning solution to the bonding surface of the wafer, and withdrawing out the wafer from the process chamber. The wafer bonding method includes the steps of: providing a first process chamber with a first wafer whose bonding surface faces upward; cleaning and surface-treating the bonding surface of the first wafer by supplying atmospheric pressure plasma and a cleaning solution to the bonding surface of the first wafer; withdrawing out the first wafer from the first process chamber and providing a second process chamber with the first wafer; providing a third process chamber with a second wafer whose bonding surface faces upward; cleaning and surface-treating the bonding surface of the second wafer by supplying atmospheric pressure plasma and a cleaning solution to the bonding surface of the second wafer; withdrawing out the second wafer from the third process chamber and providing the second process chamber with the second wafer whose bonding surface faces to the bonding surface of the first wafer and bonding the bonding surfaces of the first and second wafers to each other.