A substrate processing method and a substrate processing apparatus for selectively forming a blocking layer are provided. The substrate processing method includes: (a) preparing a substrate having a first surface including a dielectric film, a second surface including a metal nitride film, and a third surface including a conductive film, in different regions of a substrate surface; (b) supplying a first organic compound containing a thiol group, a phosphonic acid group, or a carboxylic acid group as a first reactive group to the substrate; and (c) supplying a second organic compound containing a carbon-carbon double bond or a carbon-carbon triple bond as a second reactive group to the substrate, wherein a blocking layer is formed on the second surface and the third surface selectively with respect to the first surface.