An ion implantation apparatus with multiple operating modes is disclosed. The ion implantation apparatus has an ion source and an ion extraction means for forming a converging beam on AMU-non-dispersive plane therefrom. The ion implantation apparatus includes magnetic scanner prior to a magnetic analyzer for scanning the beam on the non-dispersive plane, the magnetic analyzer for selecting ions with specific mass-to-charge ratio to pass through a mass slit to project onto a substrate. A rectangular quadruple magnet is provided to collimate the scanned ion beam and fine corrections of the beam incident angles onto a target. A deceleration or acceleration system incorporating energy filtering is at downstream of the beam collimator. A two-dimensional mechanical scanning system for scanning the target is disclosed, in which a beam diagnostic means is built in.