A semiconductor device manufacturing method has conducting first heating processing at a first heating temperature in an inert atmosphere under a first pressure in a first process chamber to silicide an upper part of the source-drain diffusion layer and form a silicide film; conducting second heating processing at a second heating temperature in an oxidizing atmosphere under a second pressure in a second process chamber to selectively oxidize at least a surface of the metal film on the element isolating insulation film and form a metal oxide film; conducting third heating processing at a third heating temperature which is higher than the first heating temperature and the second heating temperature in an atmosphere in a third process chamber to increase a concentration of silicon in the silicide film; and selectively removing the metal oxide film and an unreacted part of the metal film on the element isolating insulation film.