We fabricated a three-dimensional (3D) stacked Si nanodisk (Si-ND) array with a high aspect ratio and uniform size by using our advanced top-down technology consisting of bio-template and neutral beam etching processes. We found from conductive atomic microscope measurements that conductivity became higher as the arrangement was changed from a single Si-ND to two-dimensional (2D) and 3D arrays with the same matrix of SiC, i.e., the coupling of wave functions was changed. Moreover, our theoretical calculations suggested that the formation of minibands enhanced tunneling current, which well supported our experimental results. Further analysis indicated that four or more Si-NDs basically maximized the advantage of minibands in our structure. However, it appeared that differences in miniband widths between 2D and 3D Si-ND arrays did not affect the enhancement of the optical absorption coefficient. Hence, high photocurrent could be observed in our Si-ND array with high photoabsorption and carrier conductivity due to the formation of 3D minibands.