An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate the effects of non-additive contributions on the hydration shell structure of Mg2+. The active-site region, the sphere including the second hydration shell of Mg2+, was treated by Born-Oppenheimer ab initio quantum mechanics, while the rest is described by classical pair potentials. A hydration complex with six inner shell waters and 12 second shell waters was observed. It was also found that the effects of non-additive terms play an important role in the preferential orientation of water molecules inside the hydration sphere of Mg2+.