Abstract: Before a semiconductor substrate and a base substrate is directly bonded to one another, in a protective film removing step, a contamination protective film formed on the semiconductor substrate to protect it from contamination during an ion implanting step is removed. Consequently, even when flatness of the contamination protective film is degraded during the ion implanting step or even when contaminants remain in a segregated state in the vicinity of the surface of the contamination protective film, the state of the bonding between the semiconductor substrate and the base substrate after the bonding step can be made uniform over the entire area of the bonding. As a result, a high-quality semiconductor substrate can be manufactured at low cost.