A method of manufacturing a flip-chip light emitting diode includes: providing a transparent substrate and a temporary substrate, and bonding the transparent substrate with the temporary substrate; grinding and thinning the transparent substrate; providing a light-emitting epitaxial laminated layer having a first surface and a second surface opposite to each other, and including a first semiconductor layer, an active layer and a second semiconductor layer; forming a transparent bonding medium layer over the first surface of the light-emitting epitaxial laminated layer, and bonding the transparent bonding medium layer with the transparent substrate; defining a first electrode region and a second electrode region over the second surface of the light-emitting epitaxial laminated layer, and manufacturing a first electrode and a second electrode; and removing the temporary substrate.