The invention discloses a GaN-based light emitting diode (LED) epitaxial structure with V-pit multi-quantum well multi-wavelength and a fabrication method thereof. The structure comprises a substrate, a buffer layer, an n-type layer, an active layer and a P-type layer, wherein the buffer layer, the n-type layer, the active layer and the P-type layer are sequentially laminated on the substrate, the active layer comprises a multi-layer structure and a luminous unit, the luminous unit comprises 3-10 multi-quantum well luminous regions emitting luminous wavelengths, the multi-layer structure exists in a V pit, and the V pit generates the multi-layer structure and passes through the multi-quantum well luminous regions. Through the GaN-based light emitting diode (LED) epitaxial structure with V-pit multi-quantum well multi-wavelength, obtained according to the method, the problems of short service lifetime of fluorescent powder, high color temperature, low color rendering index, partial harm of blue-light short-wavelength and the like existing in the conventional mainstream white-light LED can be solved, and a single-chip LED without the fluorescent powder gives out white light.