A light-emitting diode and the manufacturing method thereof are provided, wherein the light-emitting diode comprises an epitaxial structure, a bonding layer and a composite substrate. The bonding layer located over one side of the epitaxial structure is used for adhering the composite substrate to the epitaxial structure. The composite substrate comprises a patterned silicon layer penetrated through by a plurality of openssilicon, and a metal layer covering the patterned silicon layer, wherein a portion of the metal layer is filled into the opens and contacts the bonding layer.