Most metals with close packed atomic arrangements have been found to adopt ABC- or AB-stacking, since this arrangement affords the largest possible coordination number of 12. Here, based on first-principles calculations, we report for the first time the predicted high stability of AA-stacked Pt nanoclusters when supported on a graphene/Ru(0001) surface. Our theoretical analysis reveals that this unusual AA stacking is favored due to chemical bonding between Pt atoms and graphene on Ru(0001) surface, where vertically aligned pz orbitals of C atoms tend to hybridize with the dz2 orbitals of the Pt atoms in the bottom most layer in the cluster. Consequently, dz2–dz2 bonding between Pt layers is induced, leading to AA-stacking sequence in the Pt nanoclusters. Further analysis proves that these supported AA-stacked Pt clusters interact with adsorbed molecules or radicals in different strength and can, therefore, serve as high-selectivity catalysts for various applications.