A manufacturing method of an SOI substrate which possesses a base substrate having low heat resistance and a very thin semiconductor layer having high planarity is demonstrated. The method includes: implanting hydrogen ions into a semiconductor substrate to form an ion implantation layer; bonding the semiconductor substrate and a base substrate such as a glass substrate, placing a bonding layer therebetween; heating the substrates bonded to each other to separate the semiconductor substrate from the base substrate, leaving a thin semiconductor layer over the base substrate; irradiating the surface of the thin semiconductor layer with laser light to improve the planarity and recover the crystallinity of the thin semiconductor layer; and thinning the thin semiconductor layer. This method allows the formation of an SOI substrate which has a single-crystalline semiconductor layer with a thickness of 100 nm or less over a base substrate.