A semiconductor device in which a metal silicide layer is formed by a salicide process is improved in reliability. By a salicide process according to a partial reaction method, metal silicide layers are formed over respective surfaces of gate electrodes, n+-type semiconductor regions, and p+-type semiconductor regions. In a first heat treatment when the metal silicide layers are formed, a heat-conduction type anneal apparatus is used for the heat treatment of a semiconductor wafer. In a second heat treatment, a microwave anneal apparatus is used for the heat treatment of the semiconductor wafer, thereby reducing the temperature of the second heat treatment and preventing abnormal growth of the metal silicide layers. Thus, a junction leakage current in the metal silicide layers is reduced.