A method of inspecting a substrate processing apparatus that enables a reduction in operator labor time to be achieved. A host computer instructs a substrate processing apparatus to prohibit transfer of a product wafer into the substrate processing apparatus during a period of cleaning the substrate processing apparatus. The substrate processing apparatus notifies the host computer of a number and types of inspection wafers to be used in inspections for predetermined inspection items. The host computer notifies the substrate processing apparatus that preparation of the inspection wafers has been completed.