The authors' assumption about the possibility of nanodomain generation in the ferroelectric LiNbO3 by relatively low energy (< 5 keV) electron beams has been experimentally confirmed. The calculated electron-induced electric fields and changes in the polarization state of the near-surface layer in the -Z cut of LiNbO3 agree with the experimental results at the energies of the primary electrons Eb = 1 and 3 keV. In the proposed four-layer model of surface charging by low-energy electrons, electron-stimulated desorption of compensating atoms and molecules from the contaminated absorbing film into a vacuum plays an important role. The presented new results confirming the formation of domains in the near-surface layer at low electron beam energy can expand the possibilities of domain engineering using electron beam technologies, especially in the field of photonics.