A method for fabricating of semiconductor device is provided, including providing a substrate. A first trench isolation and a second trench isolation are formed in the substrate. A portion of the substrate is etched to have a height between a top and a bottom of the first and second trench isolations. A germanium (Ge) doped layer region is formed in the portion of the substrate. A fluorine (F) doped layer region is formed in the portion of the substrate, lower than and overlapping with the germanium doped layer region. An oxidation process is performed on the portion of the substrate to form a gate oxide layer between the first and second trench isolations.