A substrate processing method in which processes with respect to substrates are performed comprises: stacking the substrates on a substrate holder disposed in a staking space formed within a lower chamber through a passage formed in a side of the lower chamber, exhausting the stacking space through an auxiliary exhaust port connected to the stacking space, moving the substrate holder into an external reaction tube closing an opened upper side of the lower chamber to provide a process space in which the processes are performed, and supplying a reaction gas into the process space using a supply nozzle connected to the process space and exhausting the process space using an exhaust nozzle connected to the process space and an exhaust port connected to the exhaust nozzle.