A method of manufacturing a semiconductor device having a semiconductor substrate that includes an active region for forming transistor elements, which includes a gate, and an element isolation region for isolating the transistor elements separately each other, which has a STI structure, the method comprises; first—ion implanting fist ions onto the surface of the semiconductor substrate in a region other than a stress region in the active region, which is located at the interface with the element isolation region, in the stress region, a potential stress is generated by forming the element isolation region and/or the difference between a material of the element isolation region and a material of the semiconductor substrate, so that a first impurity region for a source and/or a drain is formed in the active region in which the gate is not formed; and second ion implanting second ions each of which mass is smaller than that of each of the first ions so that a second ion impurity region is formed in the stress region.