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The effect of Ca, Pd, Sn and La atoms substitution for the central Mg atom of magnesium hydride Mg(M)H2 atom cluster on electronic structure and bonding characterization have been studied by using the discrete variational method (DVM) based on the first principles. The crystal orbital overlap population (COOP), the bond order (BO) and the bonding charge densities were analyzed by calculation. It showed that the substitution atoms Ca, Pd, Sn and La had an obvious effect on the chemical bond Mg-H which corresponds to the stable of Mg(M)H2 structure. The charge densities around their nearest neighbor Mg are redistributed and obviously anisotropic. When M is Ca, Pd or La, BO between the nearest neighbor Mg and H is almost same and increased slightly; when M is Sn, it is greatly decreased. The increased order is Sn < La < Pd < Ca. And the interactions between the other Mg atoms and hydrogen are also affected to some degree.