It is an object to provide a method of manufacturing a semiconductor device capable of forming a MOS transistor of high performance, comprising the steps of forming a gate electrode on a semiconductorsubstrate via a gate-insulating film (step S 1 ), introducing a impurity into the semiconductor substrate using the gate electrode as a mask (step S 7 ), introducing a diffusion-controlling substanceinto the semiconductor substrate to control the diffusion of the impurity (step S 8 ), forming a side wall-insulating film on each side surface of the gate electrode (step S 9 ), deeply introducing impurity into the semiconductor substrate using the gate electrode and the side wall-insulating film as masks (step S 10 ), activating the impurity by the annealing treatment using a rapid thermal annealing method (step S 11 ), and further activating the impurity by the millisecond annealing treatment (step S 12 ).