A new composite structure made of unique CuS cuboctahedron crystals and coating silica spheres with diameters ranged from 30 to 730 nm has been demonstrated. 3-Aminopropyltrimethoxysilane acted as a linker, which provided hydrogen bonding and metal-ligand bonding interaction with the facets of CuS crystals and covalent bonding of its functional silane groups onto the surface of hydrophilic silica spheres, resulting in the formation of such a CuS/silica composite structure. The suitable proportion of the amount of silica spheres and CuS crystals determined the perfection of the CuS crystals/silica composite. The successful loading of silica spheres onto the polar facets of unique CuS cuboctahedron crystals represents a new way to prepare novel composite materials with special shape.