A substrate processing method which can increase the yield by reprocessing a substrate whose processing has been interrupted by a processing interruption command during a substrate processing is disclosed. A substrate processing method performs a predetermined processing of a substrate while sequentially transporting the substrate to a plurality of processing sections according to a preset recipe. The substrate processing method includes processing a substrate in one of the processing sections; interrupting the processing of the substrate by a processing interruption command during processing of the substrate; setting the substrate whose processing has been interrupted in a standby state; and customizing the recipe and performing reprocessing of the processing-interrupted substrate according to the customized recipe, or performing reprocessing of the processing-interrupted substrate according to a preset recipe for reprocessing.