A method for cleaning a substrate processing apparatus includes mounting a substrate on a mounting portion of an electrostatic chuck of the substrate processing apparatus to process the substrate; mounting a protector including a small diameter portion that covers the mounting portion and a large diameter portion that is disposed apart from an edge ring disposed on an outer periphery of the mounting portion and has a diameter larger than that of the small diameter portion, on the mounting portion; and supplying a cleaning gas, thereby removing by-products deposited between the mounting portion and the edge ring.