One of the challenging targets in today's chemistry is size-, shape- and metal-atom packing-controlled synthesis of nano-scale transition metal cluster complexes because key factors governing these features have been elusive. Here, we present a DFT study on a recently synthesized palladium cluster complex [Pd13(μ4-C7H7)6]2+ (named Cubo-μ4; C7H7 = tropylium) with an fcc-close-packed cuboctahedral Pd13 core and possible isomers. The stability decreases in the order Cubo-μ4 > [Pd13(μ3-C7H7)3(μ4-C7H7)3]2+ with an hcp-close-packed anticuboctahedral Pd13 core (Anti-μ3,4) > [Pd13(μ3-C7H7)6]2+ with a non-close packed icosahedral Pd13 core (Ih-μ3) > [Pd13(μ4-C7H7)6]2+ with an anticuboctahedral Pd13 core (Anti-μ4) > [Pd13(μ3-C7H7)6]2+ with a cuboctahedral Pd13 core (Cubo-μ3). This ordering disagrees with the stability of the Pd13 core. The key factor governing the stability and metal-atom packing manner of these Pd13 cluster complexes is not the stability of the Pd13 core but the interaction energy between the Pd13 core and the [(C7H7)6]2+ ligand shell. The interaction energy is mainly determined by the charge-transfer from the Pd13 core to the [(C7H7)6]2+ ligand shell and the coordination mode of the C7H7 ligand (μ3- vs. μ4-coordination bond). In the μ4-coordination, all seven C atoms of the C7H7 ligand interact with four Pd atoms of the Pd4 plane using two CC double bonds and one π-allyl moiety. On the other hand, in the μ3-coordination, one or two C atoms of C7H7 cannot form bonding interaction with the Pd atom of the Pd3 plane. Thus, the use of appropriate capping ligands is one of the key points in the synthesis of nano-scale metal cluster complexes.