A film deposition method includes steps of: placing a substrate in a substrate receiving area of a susceptor provided in a vacuum chamber; evacuating the vacuum chamber; alternately supplying plural kinds of reaction gases to the substrate in the substrate receiving area from corresponding reaction gas supplying parts thereby to form a thin film on the substrate; supplying plasma including a chemical component that reacts with second reaction gas adsorbed on the substrate from a plasma generation part to the substrate when the thin film is being formed, thereby to alter the thin film on the substrate; and changing plasma intensity of the plasma supplied to the substrate, at a predetermined point of time to a different plasma intensity of the plasma that is generated and supplied to the substrate by the plasma generation part before the predetermined point of time.