A substrate processing apparatus includes: a substrate holding unit configured to hold and rotate a substrate; an etching unit configured to etch a surface of a substrate by discharging a processing liquid to the substrate rotated by the substrate holding unit; and a control unit configured to control an etching amount by the etching unit. In the substrate processing apparatus, the control unit controls an etching amount at each position on the surface of the substrate based on information upon a characteristic of a surface processing to be performed on the substrate by a post-processing apparatus which is configured to perform a post-processing after a substrate processing by the substrate processing apparatus.