A method for fabricating a semiconductor device includes: providing a substrate; forming a plurality of trenches by etching the substrate; forming a first isolation layer by filling the plurality of the trenches with a first insulation layer; recessing the first insulation layer filling a first group of the plurality of the trenches to a predetermined depth; forming a liner layer over the first group of the trenches with the first insulation layer recessed to the predetermined depth; and forming a second isolation layer by filling the first group of the trenches, where the liner layer is formed, with a second insulation layer.