A low-cost and high-throughput method for the fabrication of large-area ordered hybrid metallic nanostructure arrays is presented. Each structure unit is a nanobowl with a hexagonal distributed pillar array upon it. A self-assembled monolayer of polystyrene (PS) nanospheres is used as a template. After thermal evaporation, electroforming and removal of the nanospheres and the conductive layer, ordered arrays of hybrid nickel nanostructures have been fabricated. Both nanobowl arrays and pillar arrays exhibit uniform sizes. Smooth interior surfaces were observed in the nanobowl arrays. The geometry of the structure can be tuned by controlling the thickness of the conductive layer. The approach presented in this paper can be extended to fabricate ordered hybrid nanostructures of a wide range of metals and alloys with controlled size.