Obtaining nanoscale-ordered structures is important for the development of nanotechnology. We designed and synthesized a series of disk-cube triads containing one hexa-peri-hexabenzocoronene (HBC) and two polyhedral oligomeric silsesquioxane (POSS) moieties, HBC-2POSS. The two POSS units were linked via ester or amide bonds. With the amide linkage used, the hydrogen bonding that was introduced affected the balance between the π-π interaction of HBC cores and crystallization interaction of POSS units. Hierarchically ordered structures were obtained from HBC-2POSS triads owing to the synergistic effect of multiple secondary interactions: π-π interaction, hydrogen bonding, and crystallization interaction. As organic-inorganic hybrid materials, these HBC-2POSS triads are promising candidates for templates <10 nm.