The focus of the study was to investigate the peculiarities of the domains created by electron beam (e-beam) in a surface layer of congruent lithium niobate, which comparable to a depth of electron beam charge penetration. Direct e-beam writing (DEBW) of different domain structures with a scanning electron microscope was performed on the polar -Z cut. Accelerating voltage 15 kV and e-beam current 100 pA were applied. Different patterns of local irradiated squares were used to create domain structures and single domains. No domain contrast was observed by the PFM technique. Based on chemical etching, it was found that the vertices of the domains created do not reach the surface level. The average deepening of the domain vertices was several hundred nanometers and varied depending on the irradiation dose and the location of the irradiated areas (squares) relative to each other. Computer simulation was applied to analyze the spatial distribution of the electric field in the various irradiated patterns. The deepening was explained by the fact that in the near-surface layer there is a sign inversion of the normal component of the electric field strength vector, which controls the domain formation during DEBW. Thus, with the help of e-beam, domains were created completely located in the bulk, in contrast to the domains that are nucleated on the surface of the -Z cut during the polarization inversion with AFM tip. The detected deepening of e-beam domains suggests the possibility of creating the “head-to-head” domain walls in the near-surface layer lithium niobate by DEBW.