Provided is a substrate structure and a manufacturing method thereof, the substrate structure including a base substrate of single crystal; and a rhombohedral ferroelectric thin film exhibiting a spontaneous ferroelectric polarization and of a perovskite structure, the ferroelectric thin film being formed on a surface of the base substrate. The substrate structure may further include an optical waveguide formed on the ferroelectric thin film; and an electric field applying section that applies, to the optical waveguide, an electric field parallel to a surface of the base substrate. The electric field applying section generates the electric field so that the electric field direction of the electric field applied to the optical waveguide is parallel to a direction of the spontaneous ferroelectric polarization of the ferroelectric thin film.