A method of cleaning a silicon nitride layer on a substrate is provided to effectively remove negative-charged impurities such as polymer and particle from the silicon nitride layer. In the method, the zeta potential of the silicon nitride layer is changed from positive to negative, and then the silicon nitride layer is cleaned with a first solution selected from an alkali solution and an NC-2 solution. So the negatively-charged impurities can be easily removed due to a repulsion force. The substrate can be treated with spin scrubber or quick dump rinse before and/or after the changing of the zeta potential. To change the zeta potential, the substrate can be dipped into a second solution such as an SC-1 solution, an NC-2 solution, and an alkali solution.