There are provided a method of manufacturing a semiconductor device and a substrate processing apparatus by which the quality of a silicon nitride film can be improved. The method comprises: (a) supplying a silicon-containing gas into a process chamber accommodating a substrate in a heated state; (b) switching between an exhaust stop state and an exhaust operation state at least two times while a nitrogen-containing gas is supplied into the process chamber so as to vary an inside pressure of the process chamber such that a maximum inside pressure of the process chamber is at least twenty times higher than a minimum inside pressure of the process chamber. The steps (a) and (b) are alternately repeated to form a silicon nitride film on the substrate.