Provided are a wafer cleaning apparatus based on light irradiation capable of effectively cleaning residue on a wafer without damaging the wafer, and a wafer cleaning system including the cleaning apparatus. The wafer cleaning apparatus is configured to clean residue on the wafer by light irradiation and includes: a light irradiation unit configured to irradiate light onto the wafer during the light irradiation; a wafer processing unit configured accommodate the wafer and to control a position of the wafer such that the light is irradiated onto the wafer during the light irradiation; and a cooling unit configured to cool the wafer after the light irradiation has been completed. The light irradiation unit, the wafer processing unit, and the cooling unit are sequentially arranged in a vertical structure with the light irradiation unit above the wafer processing unit and the wafer processing unit above the cooling unit.