According to one aspect of the technique, there is provided a method of manufacturing a semiconductor device, including: (a) forming a first oxide layer by modifying a surface of a substrate at a first temperature with a plasma of a first oxygen-containing gas; and (b) forming a second oxide layer thicker than the first oxide layer by heating the substrate to a second temperature higher than the first temperature and modifying the surface of the substrate, on which the first oxide layer is formed, with a plasma of a second oxygen-containing gas.