A substrate processing apparatus includes first and second process chambers; a mounting section on which a housing vessel that houses the substrate is mounted; a vacuum transfer chamber that has a vacuum transfer machine to transfer the substrate under a negative pressure; and an atmospheric transfer chamber that has an atmospheric transfer machine that transfers the substrate under an atmospheric pressure. Timing for the atmospheric transfer chamber to take out the substrate from the housing vessel is based on a recipe remaining time, which is a remaining time of substrate processing, and an approach time, which is a time from when the substrate is taken out from the housing vessel till when the substrate is mounted to the vacuum transfer machine.