Substrate processing apparatus, substrate processing method, and semiconductor device manufacturing method

[Problem] To shorten a time needed to reduce oxygen concentration to desired concentration in a chamber to be filled with an inert gas. [Solution] This substrate processing apparatus is provided with a processing chamber for processing substrates, and a transfer chamber for transferring the substrates with respect to the processing chamber. The transfer chamber is configured to be provided with: a plurality of wall bodies that form a housing of the transfer chamber; a bonding section where the wall bodies are bonded to each other; an isolated space forming member that covers the bonding section so as to form an isolated space that is isolated from the transfer chamber; and an air release section that releases air from the isolated space.