To provide a method of manufacturing a semiconductor device, which prevents impurities from entering an SOI substrate. A source gas including one or plural kinds selected from a hydrogen gas, a helium gas, or halogen gas are excited to generate ions, and the ions are added to a bonding substrate to thereby form a fragile layer in the bonding substrate. Then, a region of the bonding substrate that is on and near the surface thereof, i.e., a region ranging from a shallower position than the fragile layer to the surface is removed by etching, polishing, or the like. Next, after attaching the bonding substrate to a base substrate, the bonding substrate is separated at the fragile layer to thereby form a semiconductor film over the base substrate. After forming the semiconductor film over the base substrate, a semiconductor element is formed using the semiconductor film.