A GaN-based LED epitaxial structure comprises a non-doped GaN buffer layer, an undoped GaN layer, an N-type GaN layer, an InGaN/GaN superlattice quantum well structure, a multiple quantum well luminous layer structure, an AlGaN layer, a low-temperature P-type layer, a P-type electron blocking layer and a P-type GaN layer which are sequentially stacked, wherein the non-doped GaN buffer layer comprises a sandwich structure consisting of a GaN layer, an AlGaN layer and a GaN layer which are sequentially stacked. For the GaN-based LED epitaxial structure and the preparation method thereof, the non-doped GaN buffer layer with the sandwich structure consisting of the GaN layer, the AlGaN layer and the GaN layer is used as a buffer layer, the buffer layer changes light scattering directions by using materials with different refractive indexes and thus the luminous efficiency can be improved.