We report the construction of dumbbell-shaped hybrid molecules for programming their hierarchical supra-molecular nanostructures through a synergetic self-assembly. Our first dumbbell-shaped hybrid molecule is a POM-organic-POSS cocluster produced by covalently coupling a POM cluster and a POSS cluster together through an organic tether. Structural analyses demonstrated a highly ordered lamellar morphology with a 4.9 tun periodicity, indicating a strong thermodynamic force driving a nanoscale phase separation of the POM and POSS blocks. The POM clusters were arranged in an orderly fashion within the POM-containing layer with a 1.38 nm periodicity because of fixed shape and size of the cluster. This investigation provides in-depth understanding of how to construct hierarchical supramolecular nanostructures at a nanoscale less than 5 nm by manipulating and controlling the topological shape of hybrid molecules.