A manufacturing method of a semiconductor device, in which a vacuum-pressure airtight chamber is defined by a space between a first substrate and a recessed portion of a second substrate, includes preparing the first substrate and the second substrate both of which contain silicon, joining the two substrates together, performing a heat treatment to emit hydrogen gas from the airtight chamber, and generating OH groups on the substrates before the joining. In the joining of the substrates together, the OH groups are bonded together to generate covalent bonds, and in the heat treatment, a part on which the OH groups are generated is heated at a temperature rise rate of 1° C. / sec or smaller until a temperature of the substrate increases to 700° C. or higher, and a heating temperature and heating time are adjusted to emit hydrogen gas from the airtight chamber.