Any particle adhesion onto the surface of a substrate to be processed is prevented. There is provided a substrate processing apparatus characterized by including a transfer chamber for, via a gate to which a substrate accommodating container for accommodation of the substrate is set, performing transfer of the substrate between the same and the substrate accommodating container, a processing chamber for applying a specific process to the substrate, a load-lock chamber for linking the processing chamber with the transfer chamber, and a temperature control unit for at the stage of transferring the substrate into at least one of the transfer chamber and the load-lock chamber, so as for the temperature of the substrate just before the transfer thereof to be higher than the temperature of the interior of the chamber, into which the substrate will be transferred, controlling at least one of the temperature of the substrate and the temperature of the interior of the chamber.