Based on the current spin density functional theory, a theoretical model of three vertically aligned semiconductor quantum dots is proposed and numerically studied. This quantum dot molecule (QDM) model is treated with realistic hard-wall confinement potential and external magnetic field in three-dimensional setting. Using the effective-mass approximation with band nonparabolicity, the many-body Hamiltonian results in a cubic eigenvalue problem from a finite difference discretization. A self-consistent algorithm for solving the Schrödinger–Poisson system by using the Jacobi–Davidson method and GMRES is given to illustrate the Kohn–Sham orbitals and energies of six electrons in the molecule with some magnetic fields. It is shown that the six electrons residing in the central dot at zero magnetic field can be changed to such that each dot contains two electrons with some feasible magnetic field. The Förster–Dexter resonant energy transfer may therefore be generated by two individual QDMs. This may motivate a new paradigm of Fermionic qubits for quantum computing in solid-state systems.