The disclosure relates to an electronic beam machining system. The system includes a vacuum chamber; an electron gun located in the vacuum chamber and used to emit electron beam; a holder located in the vacuum chamber and used to fix an object; a control computer; and a diffraction unit located in the vacuum chamber; the diffraction unit includes a two-dimensional nanomaterial; the electron beam transmits the two-dimensional nanomaterial to form a transmission electron beam and a plurality of diffraction electron beams; the transmission electron beam and the plurality of diffraction electron beams radiate the object to form a transmission spot and a plurality of diffraction spots.