A substrate processing apparatus includes: a carrier block including first and second carrier placement units spaced apart in a right and left direction; a processing block having a layered structure in which a plurality of layered parts are vertically arranged, the layered parts each including a substrate transport mechanism for transporting a substrate and a processing module for processing a substrate; a tower unit including plural substrate placement units located at height positions where a substrate is transferred by the substrate transport mechanism of the layered part corresponding to the substrate placement unit; a first substrate transfer mechanism configured to transfer a substrate between the carrier on the first carrier placement unit and the substrate placement unit of the tower unit; and a second substrate transfer mechanism configured to transfer a substrate between the carrier on the second substrate placement unit and the substrate placement unit of the tower unit.