A method for manufacturing a semiconductor device includes forming a first trench and a second trench in a substrate, the first and the second trenches communicate with each other, the second trench may be formed wider than the first trench; forming a liner layer over an inner surface of the first trench and over an inner surface of the second the trench; forming a capping layer over the liner layer to form a merged overhang and a non-merged overhang, the merged overhang may be fill a top portion of the first trench, the non-merged overhang may be open a top portion of the second trench; and forming a gap-fill layer over the capping layer to fill a lower portion of the first trench and the second trench.