In a method of manufacturing a semiconductor device including a Fin FET, a fin structure, which has an upper fin structure made of SiGe and a bottom fin structure made of a different material than the upper fin structure, is formed, a cover layer is formed over the fin structure, a thermal operation is performed on the fin structure covered by the cover layer, and a source/drain epitaxial layer is formed in a source/drain region of the upper fin structure. The thermal operation changes a germanium distribution in the upper fin structure.