Copper-based nanomaterials have attracted tremendous interest due to their unique properties in the fields of photoluminescence and catalysis. As a result, studies on the correlation between their molecular structure and their properties are of great importance. Copper nanoclusters are a new class of nanomaterials that can provide an atomic-level view of the crystal structure of copper nanoparticles. Herein, a high-nuclearity copper nanocluster with 81 copper atoms, formulated as [Cu81(PhS)46(tBuNH2)10(H)32]3+ (Cu81), was successfully synthesized and fully studied by X-ray crystallography, X-ray photoelectron spectroscopy, hydrogen evolution experiments, electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy, and density functional theory calculations. Cu81 exhibits extraordinary structural characteristics, including (i) three types of novel epitaxial surface-protecting motifs; (ii) an unusual planar Cu17 core; (iii) a hemispherical shell, comprised of a curved surface layer and a planar surface layer; and (iv) two distinct, self-organized arrangements of protective ligands on the curved and planar surfaces. The present study sheds light on structurally unexplored copper nanomaterials and paves the way for the synthesis of high-nuclearity copper nanoclusters.