The invention discloses a method for manufacturing a semiconductor device. The method comprises the steps of preparing a wafer which is formed on a substrate and contains a plurality of bosses, wherein the bosses protrude at a surface of the substrate and has a height measured from the surface of the substrate; determining interval distribution which represents spaced distribution between the adjacent bosses; calculating an implantation angle based on the height and the interval distribution, wherein the implantation angle is an angle between a normal direction and an implantation direction of the substrate; and carrying out ion implantation according to the calculated implantation angle.