Polyhydrido copper nanoclusters are an emerging class of nanomaterials. Unfortunately, insights into the structural evolution and structure–property relationship of such copper nanoclusters are scant, because of the difficulty of synthesizing and crystallizing nanoclusters with high nuclearity and new morphologies. Here, we report an anisotropic cuboidal polyhydrido copper nanocluster, [Cu23(PhSe)16(Ph3P)8(H)6]·BF4, with a distorted cuboctahedral Cu13 core stabilized by two square protecting motifs and six hydrides. The cuboidal nanoclusters self-assemble into a quasi-simple cubic packing pattern with perfect face-to-face contact of neighboring nanoclusters and interdigitation of intercluster surface ligands. Atomic-level observations reveal the crucial role that subtle synergies between nanocluster geometry and intercluster noncovalent interactions play in guiding nanocluster self-assembly. In addition, a comparison with previously reported analogous metal nanoclusters points to bulky monodentate phosphine ligands as a potent inducing agent for the formation of rectangular hexahedral nanoclusters. These findings have significant implications for the controllable synthesis of polyhedral nanomaterials and their superstructures.