The invention relates to a manufacturing method of a semiconductor device. A substrate in which an insulating layer, a semiconductor layer and an insulating film are stacked on a semiconductor substrate and an element isolation region is embedded in a trench is prepared. After the insulating film in a bulk region is removed by dry etching and the semiconductor layer in the bulk region is removed by dry etching, the insulating layer in the bulk region is thinned by dry etching. A first semiconductor region is formed in the semiconductor substrate in a SOI region by ion implantation, and a second semiconductor region is formed in the semiconductor substrate in the bulk region by ion implantation. Then, the insulating film in the SOI region and the insulating layer in the bulk region are removed by wet etching. Thereafter, a first transistor is formed on the semiconductor layer in the SOI region and a second transistor is formed on the semiconductor substrate in the bulk region.