On the basis of structural analysis by the bond valence model, it is microscopically found that intrinsic defects in lithium niobate (LN) single crystals lead to a local contraction around Nb Li 4+ –□ Li sites (□ Li means a vacant site at the original Li-site). The domain engineering of LN crystals depends strongly on the defect concentration induced in the crystallographic frame, due to that the domain switching is directly governed by the frame deformation of constituent octahedra. A kinetic model of the polarization process is proposed in an atomistic scale on the basis of the basic structure of LN crystals, which gives a clear perspective on the mechanism of polarization and a good understanding the role of point defects in domain engineering. Some observed phenomena in domain engineering may be well interpreted in this work.