There is provided a technique capable of forming a sufficiently flat film. According to one aspect of the technique, there is provided a substrate processing method including: forming a metal-containing multi-layer film structure on a substrate by alternately performing: (a) forming a metal-containing film on the substrate; and (b) supplying a process gas to the substrate so as to perform one or both of (b-1) forming a crystal layer separation film to a surface of the metal-containing film and (b-2) removing abnormal growth nuclei at the surface of the metal-containing film.