Provided is that the method of manufacturing the semiconductor device including a first process of implanting a first impurity of a first conductivity type in a source and drain region having an elevated structure, with a concentration equal to or less than 1E14 atoms/cm2, on the conditions that the concentration peak thereof is located more deeply than the interface between silicide and a semiconductor substrate, a second process of implanting a second impurity of a first conductivity type having a smaller mass than that of the first impurity in the source and drain region on the conditions that the peak thereof is located more shallowly than the concentration peak of the first impurity, and a third process of applying high-temperature millisecond annealing to the semiconductor substrate after the first and second processes.