A method of manufacturing a semiconductor device includes: a bonding step of bonding a first substrate with optical transparency and a second substrate having a surface on which a functional element is provided to each other such that the functional element faces the first substrate; a thinning step of thinning at least one of the first and second substrates; and a through-hole forming step of forming a cavity and a through-hole communicated with the cavity in at least part of a bonding portion between the first and second substrates. According to the present invention, it is possible to prevent irregularities or cracks caused by the presence or absence of the cavity and more regularly thin the substrate. In addition, it is possible to manufacture a semiconductor device capable of contributing to the miniaturization of devices and electronic equipment having the devices, using a more convenient process.