Generally, the crystal growth morphology in liquid or vapor was controlled by chemical potential, while that in solid solute was restricted by 3D strain matching between matrix and secondary phase. It is already known that the growth and evolution of the morphology of secondary phase during the solid phase transformation are highly determined by the variation of interface energy induced by lattice mismatch. In this work, the growth morphology and crystallography of Hg5In2Te8 precipitates in Hg3In2Te6 matrix were investigated by means of transmission electron microscopy (TEM). It was found that the growth of Hg5In2Te8 precipitates displayed an unusual growth morphology which contain three crystallographically equivalent variants with different growth directions in Hg3In2Te6 matrix, suggesting a slight lattice constant variation of Hg5In2Te8 precipitate during the phase transformation at high temperature, which is different from the previous reports on the crystal structures of Hg5In2Te8. According to the near coincident site lattice calculation, the changes in lattice constant of the precipitate were confirmed to shrink 0.7577%. The vacancy ordering phenomena along the directions of 3 basal axes in Hg5In2Te8 is fully attributed to such lattice shrinkage. By considering the interface energy, lattice spacing and lattice plane density, it was found that the migration velocity of the growth interface between matrix and precipitate tended to increase along the certain lattice shrinkage directions, leading to the preferred growth directions of Hg5In2Te8 precipitates. Furthermore, the crystallographic characteristics calculated by using invariant deformation element model for all the 3 variants of Hg5In2Te8 precipitate and matrix had a good agreement with the experimental results.