When a step is delayed, an operator can be rapidly informed of the delay. A substrate processing apparatus comprises a process system configured to process a substrate; a control unit configured to control the process system for performing a plurality of steps; and a manipulation unit configured to monitor a progress of each of the plurality of steps, wherein when a time elapsed after the control unit goes into a hold state exceeds an allowable time previously allocated to the one of the plurality of steps while waiting for a completion of the one of the plurality of steps started by the process system, the control unit transmits an alarm message to the manipulation unit so as to inform the manipulation unit that the allowable time is exceeded, terminates the hold state, and performs a recovery action.