An epitaxial substrate for growing a lighting emitting structure of a light emitting diode, includes a transparent base, a first buffer layer and a second buffer layer formed on the transparent base. The transparent base includes a first surface and a second surface opposite to the first surface. Plural protrusions are formed on the first surface of the transparent base. Each first buffer layer is formed on the outer surfaces of the plural protrusions. The second buffer layer fills in the recesses defined between two adjacent protrusions, and covers the first buffer layer. The refractive index of the first buffer layer is larger than that of the transparent base, and is less than that of the second buffer layer. This disclosure also relates a method for manufacturing the epitaxial substrate and a light emitting diode having the same.