Provided is a substrate processing apparatus. The apparatus includes: a process vessel, a heater, a source gas supply system, an oxygen-containing gas supply system, a hydrogen-containing gas supply system, a pressure regulator, and a controller. The controller is configured to control the parts so as to perform: (a) forming an oxide film on a substrate by alternately repeating: (a-1) forming a layer by supplying a source gas into the process vessel accommodating the substrate; and (a-2) changing the layer into an oxide layer by supplying an oxygen-containing gas and an hydrogen-containing gas into the process vessel, the inside of the process vessel being under a heated atmosphere having a low pressure; and (b) modifying the oxide film formed on the substrate by supplying the oxygen-containing gas and the hydrogen-containing gas into the process vessel, the inside of the process vessel being under the heated atmosphere having the low pressure.