A method for forming a gate oxide layer on a substrate is provided, in which a region of the substrate is defined out by a shallow trench isolation (STI) structure. An oxide layer covers over the substrate and a mask layer with an opening to expose oxide layer corresponding to the region with an interface edge of the STI structure. The method includes forming a silicon spacer on a sidewall of the opening. A cleaning process is performed through the opening to expose the substrate at the region. An oxidation process is performed on the substrate at the region to form the gate oxide layer, wherein the silicon spacer is also oxidized to merge to an edge of the gate oxide layer.