According to an embodiment, a substrate treatment apparatus includes a support unit, a silane coupler supplier, an organic functional group remover, and a drive mechanism. The support supports a substrate having a patterned film. The silane coupler supplier supplies the film with a silane coupler. The organic functional group remover removes an organic functional group from the film silylated with the silane coupler. The drive mechanism drives at least one of the support, the silane coupler supplier, and the organic functional group remover in such a way that the supply of the silane coupler and the supply of light or gas are repeated by a predetermined number.