It is an object to provide a homogeneous semiconductor substrate in which defective bonding is reduced. Such a semiconductor substrate can be formed by the steps of: disposing a first substrate in a substrate bonding chamber which includes a substrate supporting base where a plurality of openings is provided, substrate supporting mechanisms provided in the plurality of openings, and raising and lowering mechanisms which raise and lower the substrate supporting mechanisms; disposing a second substrate over the first substrate so as not to be in contact with the first substrate; and bonding the first substrate to the second substrate by using the raising and lowering mechanisms to raise the substrate supporting mechanisms.