Magic-sized clusters, as the intermediate state between molecules and nanoparticles, exhibit critical transitions of structures and material properties. We report two unique structures of gold clusters solved by x-ray crystallography, including Au₄₀ and Au₅₂ protected by thiolates. The Au₄₀ and Au₅₂ clusters exhibit a high level of complexity, with the gold atoms in the cluster first segregated into four-atom tetrahedral units—which then coil up into a Kekulé-like ring in the Au₄₀ cluster and a DNA-like double helix in Au₅₂. The solved structures imply a new “supermolecule” origin for revealing the stability of certain magic-sized gold clusters. The formation of supermolecular structures originates in the surface ligand bonding–induced stress and its propagation through the face-centered cubic (FCC) lattice. Moreover, the two structures reveal anisotropic growth of the FCC lattice in the cluster regime, which provides implications for the important roles of ligands at the atomic level. The rich structural information encoded in the Au₄₀ and Au₅₂ clusters provides atomic-scale insight into some important issues in cluster, nanoscale, and surface sciences.