A method of manufacturing a light emitting diode element is provided. A first patterned semi-conductor layer, a patterned light emitting layer, and a second patterned semi-conductor layer are sequentially formed on an epitaxy substrate so as to form a plurality of epitaxy structures, wherein the first patterned semi-conductor layer has a thinner portion in a non-epitaxy area outside the epitaxy structures. A passivation layer covering the epitaxy structures and the thinner portion is formed. The passivation layer covering on the thinner portion is partially removed to form a patterned passivation layer. A patterned reflector is formed directly on each of the epitaxy structures. The epitaxy structures are bonded to a carrier substrate. A lift-off process is performed to separate the epitaxy structures from the epitaxy substrate. An electrode is formed on each of the epitaxy structures far from the patterned reflector.