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.