The invention relates to a flip light-emitting diode structure and a manufacturing method thereof. The flip light-emitting diode structure comprises a substrate, an epitaxial layer, at least one opening structure and an insulation layer. The epitaxial layer is located on the substrate, and the epitaxial layer comprises a first semiconductor layer, a second semiconductor body and a luminous layer arranged between the first semiconductor layer and the second semiconductor body. The opening structures are located at the edge position of the epitaxial layer and extend to the surface of the substrate so as to enable the lateral wall of a part of the epitaxial layer and the surface of a part of the substrate to be exposed, and therefore the epitaxial layer is divided into a main epitaxial layer and a barrier gate structure. The insulation layer is located on the opening structures and serves as a metal electrode insulation layer.