Crystals of laihunite from Xiaolaihe of Liaoning Province, northeast China, were studied using selected-area electron diffraction (SAED), high-resolution transmission electron microscopy (HRTEM), and Z-contrast imaging. Z-contrast images directly reveal ordered vacancies in M1 sites. The results confirm early structural models for 1-layer laihunite (or laihunite-1M) with ideal stoichiometry of □_0.5Fe²⁺_0.5Fe ³⁺SiO₄. 2-layer laihunite and 3-layer laihunite are found to be chemically different from laihunite-1M. The 2-layer laihunite can be viewed as a periodic intergrowth of laihunite and fayalite in the 1:1 ratio. The 3-layer laihunite can be considered to be a periodic intergrowth of laihunite and fayalite in the 1:0.5 ratio along the c-axis. Ideal stoichiometries for the 2-layer structure and the 3-layer structure are □_0.5Fe ²⁺_2.5Fe³⁺[SiO₄]₂ and □_1.0Fe²⁺_3.0Fe³⁺ _2.0[SiO₄]₃, respectively. The structural intergrowth of the 3-layer laihunite and the 1-layer lahunite results in chemical compositions falling within the range between the two aforementioned structures, such as the chemical formula of □_0.4Fe ²⁺_0.8Fe³⁺_0.8SiO₄, reported earlier in the literature. The crystal structures of the 1-layer laihunite (1M), the 2-layer laihunite (2M), and the 3-layer laihunite (3Or) determined from Z-contrast images and ab initio calculations using the density functional theory (DFT) have space groups of P2₁/b, P2₁/b, and Pbnm, respectively. The previously reported monoclinic symmetry for the 3-layer laihunite may be an artifact due to overlapping diffraction spots from both, the laihunite-3Or and the laihunite-1M. Our study demonstrates that the method of combining Z-contrast imaging and ab initio calculation can be effectively used for identifying structures of nano-phases in host crystals. Perhaps more importantly, Z-contrast imaging provides a powerful means for direct observation of vacancies and other defects, and may be utilized to map vacancies in Fe³⁺-bearing olivines, the alignments of which can greatly affect anisotropic diffusion in such structures.