Understanding the electric dipole switching in multiferroic materials requires deep insight of the atomic-scale local structure evolution to reveal the ferroelectric mechanism, which remains unclear and lacks a solid experimental indicator in high-pressure prepared LiNbO3-type polar magnets. Here, we report the discovery of Zn-ion splitting in LiNbO3-type Zn2FeNbO6 established by multiple diffraction techniques. The coexistence of a high-temperature paraelectric-like phase in the polar Zn2FeNbO6 lattice motivated us to revisit other high-pressure prepared LiNbO3-type A2BB'O6 compounds. The A-site atomic splitting (∼1.0-1.2 Å between the split-atom pair) in B/B'-mixed Zn2FeTaO6 and O/N-mixed ZnTaO2N is verified by both powder X-ray diffraction structural refinements and high angle annular dark field scanning transmission electron microscopy images, but is absent in single-B-site ZnSnO3. Theoretical calculations are in good agreement with experimental results and suggest that this kind of A-site splitting also exists in the B-site mixed Mn-analogues, Mn2FeMO6 (M = Nb, Ta) and anion-mixed MnTaO2N, where the smaller A-site splitting (∼0.2 Å atomic displacement) is attributed to magnetic interactions and bonding between A and B cations. These findings reveal universal A-site splitting in LiNbO3-type structures with mixed multivalent B/B', or anionic sites, and the splitting-atomic displacement can be strongly suppressed by magnetic interactions and/or hybridization of valence bands between d electrons of the A- and B-site cations.