A substrate processing method includes step a), step b), step c), step d), step e), and step f). Step a) is a step of providing a substrate that has a pattern where a protection target film is positioned on a bottom part of the pattern. Step b) is a step of laminating a catalyst film on the protection target film. Step c) is a step of forming a protection film that supports the catalyst film from below and covers the protection target film, in the pattern, by a VLS growth method. Step d) is a step of removing the catalyst film. Step e) is a step of applying a predetermined process to a part of the substrate that is different from the pattern in a state where the protection target film is covered by the protection film. Step f) is a step of removing the protection film in the pattern.