A cleaning method for improving a wafer surface polluted by metal ions is disclosed. This method is to install an ion change filter in a pipeline, in which deionized water runs, to reduce the number of metal ions to be less than 0.1 ppb, so as to avoid that the metal ions of deionized water remains on the surface of the wafer during the process in cleaning the wafer and diffuses in the thermal oxidation process afterwards to affect the quality of oxide film.