This work aims at understanding the formation and stability of a layered structure of brucite mineral [Mg(OH)2] via density functional calculations. Because Mg–O–Mg bond formation from a hydrolyzed species of Mg(II) ion is a critical elemental step of mineralization, we studied the reaction mechanism of Mg–O–Mg linkage using a model cluster, [Mg(OH)2]n (n = 1–10), in the gas phase and a water solution. The results indicate that no barrier exists during the reaction path from [Mg(OH)2]n−1 + Mg(OH)2 to [Mg(OH)2]n with no significant solvent effect of water. It has been confirmed that this polymerization reaction leads spontaneously to a planar cluster, which is regarded as a part of the brucite layer. The results suggest that the layered structure of brucite is a natural consequence of polymerization. These findings will be utilized to establish microscopic modeling for studying a templating effect on the formation of an inorganic thin film.