The embodiment of the invention discloses a patterned composite substrate, a preparation method and an LED epitaxial wafer. Wherein the substrate comprises a sapphire substrate; the plurality of microstructure protrusions are located on the sapphire substrate, the microstructure protrusions comprise fluorine-doped silicon dioxide, and the refractive index of the fluorine-doped silicon dioxide is smaller than that of silicon dioxide. According to the patterned composite substrate, the preparation method thereof and the LED epitaxial wafer provided by the invention, the microstructure bulges made of the fluorine-doped silicon dioxide material are prepared above the sapphire substrate, and the refractive index of the fluorine-doped silicon dioxide material is lower, the refractive index difference between the substrate and the epitaxial layer material is larger, and the total reflection angle is increased, so that the light extraction rate can be improved; and the brightness of the epitaxial end and the chip end is improved. In addition, compared with a traditional silicon dioxide substrate material, the fluorine-doped silicon dioxide substrate material with the low refractive index is easier to etch under the same condition, the etching speed is high, the etching selection ratio is higher, and the productivity of dry etching can be improved.