The invention relates to a preparation method for a small silicon-based nano hollow array with orderly heights, belonging to the technical field of nano-structure preparation. The preparation method employs large-diameter polystyrene nano-spheres which are self-mounted into a single-layer nano-sphere film serving as masks on a Si substrate. After going through multiple technical procedures such as reaction ion lithography, direct current sputtering metal films, selective corrosion and the like, the mask is converted into a small inverted-pyramidal nano-hollow array, which is a two-dimensionalhexagonal dot array. The cycle of the nano-hollow arrays is determined by the diameters initially selected for the polystyrene nano-spheres. The invention is likely to be used in fields of growth of controllable quantum structures, photonic crystal manufacturing, quantum logic operation, magnetic storage media, etc.