A light emitting diode (LED) structure includes a substrate with a surface and cylindrical photonic crystals, a first type doping semiconductor layer, a first electrode, a light emitting layer, a second type doping semiconductor layer and a second electrode. The first type doping semiconductor layer is formed on the substrate to cover the photonic crystals. The light emitting layer, the second type doping semiconductor layer and the second electrode are sequentially formed on a portion of the first type doping semiconductor layer. The first electrode is formed on the other portion of the first type doping semiconductor layer without being covered by the light emitting layer. Because the substrate with photonic crystals can improve the epitaxial quality of the first type doping semiconductor layer and increase the energy of the light forwardly emitting out of the LED, the light emitting efficiency of the LED is effectively enhanced.