We have synthesized single crystals of a highly stable Cu6 nanocluster protected by six ligands of 2-mercapto-5-n-propylpyrimidine (SMPP). This Cu6(SMPP)6 cluster has a quasi-octahedral superatomic Cu6 core, with the Cu atoms being protected by both -S- and N-bidentate coordination of the SMPP ligands. Interestingly, each Cu atom is linked with an N atom, while the two neighboring Cu atoms on the same triangular facet are linked by the -S- bridge of the ligand. Single-crystal parsing results show that the altered orientation of the SMPP ligands give rise to three packing modes (named as 1, 2, and 3) of the Cu6(SMPP)6 NCs. Apart from the well-organized coordination, this Cu6(SMPP)6 nanocluster exhibits superatomic stability with a metallic core of 4 valence electrons (1S22S2||3S2), enabling to largely balance the interactions between the polynuclear core and delocalized electrons. Interestingly, the Cu6(SMPP)6 NCs display dual emissions in both ultraviolet-visible (UV-Vis) and near-infrared (NIR) regions. First-principles calculations well reproduce the experimental spectrum, shedding light on the nature of excitation states and metal-ligand interactions in the Cu6(SMPP)6 cluster.