A method of processing a substrate includes: substituting a functional group with a hydroxyl group by heating a substrate on which a SiN film containing a silicon compound having the functional group composed of nitrogen and hydrogen is formed while supplying a first processing gas containing at least one of H2O2 or H2O to the substrate; and subsequently obtaining a SiO film by heating the substrate to desorb the hydrogen from the silicon compound while supplying, in a plasma state, a second processing gas including at least one of O2 or O3 to the substrate.