A substrate processing method and a substrate processing apparatus are provided, which solve problems of pattern collapse and particles. The substrate processing method includes: a surface modification step of modifying a surface of a substrate having an oxide thereon to improve or reduce roughness of the surface; a surface cleaning step of supplying a treatment liquid to the modified surface of the substrate to clean the surface of the substrate with the treatment liquid; and a hydrophobization step of supplying a hydrophobizing agent to the cleaned surface of the substrate to hydrophobize the surface of the substrate.