A method of manufacturing a nanostructure semiconductor light emitting device including providing a base layer formed of a first conductivity type semiconductor. A mask including an etch stop layer is formed on the base layer. A plurality of openings are formed in the mask so as to expose regions of. A plurality of nanocores are formed by growing the first conductivity type semiconductor on the exposed regions of the base layer to fill the plurality of openings. The mask is partially removed by using the etch stop layer to expose side portions of the plurality of nanocores. An active layer and a second conductivity type semiconductor layer are sequentially grown on surfaces of the plurality of nanocores.