According to the substrate processing method in the embodiments, as a mask substrate used for forming an EUV mask, a mask substrate in which a first film having a first hydrophilicity is formed on one main surface and a resist is applied to another main surface is exposed from a side of the resist. Then, a hydrophilic treatment is performed on a surface of the first film to make the surface of the first film have a second hydrophilicity larger than the first hydrophilicity. Then, a development treatment of the resist is performed with respect to the mask substrate in which the hydrophilic treatment is performed on the surface of the first film to have the second hydrophilicity.