In a substrate processing apparatus using a neutralized beam and a method thereof, the substrate processing apparatus includes: an ion source for emitting an ion beam at an emitting angle; reflectors at which the ion beam emitted by the ion source is incident and subject to 2n collisions (where n is a positive integer) in first and second opposite directions to neutralize the ion beam as a neutralized beam and to restore a direction of propagation of the neutralized beam to the emitting angle of the ion beam; and a substrate at which the neutralized beam generated by the reflectors is incident on to perform a process. Accordingly, an incident angle of the resultant neutralized beam is perpendicular to a substrate, while the direction of propagation of the originating ion source and the surface of the substrate are maintained to be perpendicular to each other.