A substrate processing apparatus includes a chamber, a pedestal provided in the chamber and having a substrate holding region to hold a substrate thereon, and a gas supply part to supply a gas into the chamber. A plurality of electron gun arrays two-dimensionally arranged so as to cover the substrate holding region is provided and configured to emit electrons toward the gas to cause interactions between the emitted electrons and the gas. A plurality of electron energy control parts is correspondingly provided at each of the electron gun arrays and configured to control energy of the electrons emitted from each of the electron gun arrays independently of each other.