There is provided a method of manufacturing a nanostructure semiconductor light emitting device including providing a base layer formed of a first conductivity-type semiconductor, forming a mask including an etch stop layer on the base layer, forming a plurality of openings with regions of the base layer exposed therethrough, in the mask; forming a plurality of nanocores by growth of the first conductivity-type semiconductor on the exposed regions of the base layer to fill the plurality of openings, partially removing the mask using the etch stop layer to expose side portions of the plurality of nanocores, and sequentially growth of an active layer and a second conductivity-type semiconductor layer on surfaces of the plurality of nanocores.