A high-quality Si nanodisk superlattice is fabricated by our top-down process. For the first time, a 3D finite element method (FEM) is developed to calculate energy band structure, optical and electrical properties, as well as the intermediate band solar cell (IBSC) operation for the realistic structure. Both the experiments and simulations reveal that miniband formation enhances the optical and electrical collections. Consequently, detailed electronic structure and conversion efficiency are examined to guide optimal design of minibands. A theoretically predicted maximal efficiency of the explored Si nanodisk superlattice is 50.3%, which is promising, compared with well-known complicated Si tandem solar cells.