Abstract: A LED epitaxial-Chip with patterned GaN based substrate is provided. The LED epitaxial-Chip includes a substrate, a butter layer formed on the substrate, unintentional doped intrinsic GaN layer formed on the substrate, n-GaN layer formed on the substrate, InGaN active layer formed on the substrate, multiple quantum well formed on the substrate; and p-GaN layer formed on the sapphire substrate. The substrate has DBR reflection layer formed thereon. The DBR reflection layer is layered structure grown by two materials having different refractive index periodically alternate. The reflection layer forms at least two spaced patterned structures on the substrate. A manufacturing method of LED epitaxial-Chip with patterned GaN based substrate is also provided.