A thin film deposition apparatus includes: a deposition source that discharges a deposition material; a deposition source nozzle unit disposed at a side of the deposition source and including a plurality of deposition source nozzles arranged in a first direction; a patterning slit sheet disposed opposite to the deposition source nozzle unit and including a plurality of patterning slits arranged in the first direction; a position detection member that detects a relative position of the substrate to the patterning slit sheet; and an alignment control member that controls a relative position of the patterning slit sheet to the substrate by using the relative position of the substrate detected by the position detection member, wherein the thin film deposition apparatus and the substrate are separated from each other, and the thin film deposition apparatus and the substrate are moved relative to each other.