A method of inspecting a substrate processing apparatus, which is capable of preventing product substrates from being supplied to a substrate processing chamber to be inspected, and inspecting the substrate processing chamber in desired timing. Product wafers W (product substrates) are inhibited from being conveyed into a processing unit to be inspected (substrate processing chamber) according to a selection of a menu option “QC MODE” by an operator, or in response to instruction from a host computer. A QC wafer is permitted to be conveyed from a carrier connected to an associated load port 24 into the processing unit to be inspected, in response to a notification the fact that a wafer stored in the carrier connected to the associated load port 24 is the QC wafer.