A shape amphiphile composed of covalently linked spherical and cubic nanoparticles with distinct symmetry ([60]fullerene (C60) and polyhedral oligomeric silsesquioxane (POSS)) was synthesized and its solid state structures were characterized. The two types of nanoparticles are known to be generally immiscible, but they were connected with a short covalent linkage forming an organic–inorganic dyad (POSS–C60) which exhibited interesting crystallization characteristics. Crystals of the dyad exhibited polymorphism with two different crystal structures: an orthorhombic and a hexagonal unit cell with symmetry groups of P21212 and P6, respectively, both of which formed an alternating bi-layered structure of POSS and C60. The different symmetry groups in the polymorphs were attributed to the different packing orientations of the POSS within each layer. In the orthorhombic unit cell, one set of the edges of the POSS moieties is parallel to the c-axis; while in the hexagonal unit cells the body-diagonal is parallel to the c-axis of the crystal. Based on the crystal packing structure and density differential, it has been determined that the hexagonal unit cell structure is the more thermodynamically stable phase. This type of bi-layered structure with an alternating conductive fullerene and insulating POSS layer structure is of great interest for various potential applications such as nano-capacitors.