An apparatus and method for processing a surface of a substrate using neutral beams are provided to repeatedly process an oxide layer using the neutral beams having low energy to minimize electrical damage to the oxide layer and improve characteristics of the oxide layer. The apparatus is mounted in a plasma generating chamber, and includes: an ion beam generating gas inlet, which injects a gas for generating ion beams; an ion source, which generates the ion beams having a polarity from the gas introduced through the ion beam generating gas inlet; a grid assembly, which is installed on one end of the ion source; a reflector, which is aligned with the grid assembly and converts the ion beams to the neutral beams; and a stage, on which the substrate is placed on a traveling path of the neutral beams.