The present disclosure provides a substrate processing apparatus including: a substrate processing chamber configured to process a substrate on which a target layer to be removed is formed on the surface of an underlying layer; a substrate holding unit provided in the substrate processing chamber and configured to hold the substrate; a mixed liquid supplying unit configured to supply a mixed liquid of sulfuric acid and hydrogen peroxide to the substrate held by the substrate holding unit in a mixing ratio of the hydrogen peroxide and a temperature that does not damage the underlying layer while removing the target layer; and an OH-group supplying unit configured to supply a fluid containing OH-group to the substrate in an amount that does not damage the underlying layer when the mixed liquid and the OH-group are mixed on the substrate.