A flip-chip light emitting diode, including a substrate, an N-type semiconductor layer, a light emitting layer and a P-type semiconductor layer series mounted along a height direction of the flip-chip light emitting diode. A P electrode is formed on the P-type semiconductor layer and an N electrode is formed on the N-type semiconductor. A top surface of the substrate is away from the light emitting layer. A plurality of micron main portions is formed on the top surface. An outer surface of each main body has a plurality of nanometer protrusions. A method for manufacturing the flip chip light emitting diode is also provided.