A substrate processing apparatus includes: a substrate holder to vertically load a plurality of substrates in multiple stages with an interval therebetween and including a plurality of partition plates vertically partitioning a region where the plurality of substrates are loaded; a process chamber to receive the substrate holder therein; protrusions protruding inward toward the outer circumferential surfaces of the partition plates from an inner circumferential wall surface within the process chamber, which faces the outer circumferential surfaces of the partition plates, to form clearances between inner circumferential surfaces formed on the protruding tip ends of the protrusions and the outer circumferential surfaces of the partition plates; and a gas supply part to supply inert gas into the clearances, which are formed between the inner circumferential surfaces of the protrusions and the outer circumferential surfaces of the partition plates, to form positive-pressure sections subjected to a pressure higher than ambient pressure.