A high-current, mass-separated low energy ion beam deposition system with dual ion sources, which utilizes acceleration-deceleration method, has been developed to create new functional materials, especially those having multi-layered structure. In this system, the maximum ion currents obtained at the ion energy of 100 eV are 5.1 mA for Ar+ ions and 5.3 mA for Ca+ ions. The deceleration characteristics in the high current region at the ion energy below 100 eV are described. Epitaxial growth of alpha-Fe film on the Si(111) substrate has been also carried out at room temperature using this system. The dependence of beam diameter on Fe+ ion current and the dependence of the film quality on Fe+ ion energy are discussed.