A substrate processing apparatus, including: a reaction container in which a substrate is processed; a seal cap, brought into contact with one end in an opening side of the reaction container via a first sealing member and a second sealing member so as to seal the opening of the reaction container air-tightly; a first gas channel, formed in a region between the first sealing member and the second sealing member in a state where the seal cap is in contact with the reaction container; a second gas channel, provided to the seal cap and through which the first gas channel is in communication with an inside of the reaction container; a first gas supply port that is provided to the reaction container and supplies a first gas to the first gas channel; and a second gas supply port that is provided to the reaction container and supplies a second gas into the reaction container, wherein a front end opening of the first gas supply port opening to the first gas channel, and a base opening of the second gas channel opening to the first gas channel being separated from each other in a state where the seal cap is in contact with the reaction container.