We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai–Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by Conquest, and the eigenstates of the Hamiltonians are then obtained by the Sakurai–Sugiura method. Applications to a hydrated DNA system and adsorbed P₂ molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.