We have developed numerical simulation method for quasi-particle structures in the three-dimensional nano-sized superconductors, using the three-dimensional finite element method and the Bogoliubov-de Gennes equation. Using this method, we analyzed the superconducting state in the nano-sized cubic superconductors. We found the spatial oscillations of order parameter because of the confinement of superconducting electrons, and also we found the quasi-particle bound states at the corners of the cubic superconductors because of suppression of superconductivity at the corners.