The invention provides a light emitting diode epitaxial wafer and a manufacturing method thereof, and belongs to the technical field of semiconductors. The light emitting diode epitaxial wafer comprises a substrate, and a low-temperature buffer layer, a high-temperature buffer layer, an N-type layer, a multi-quantum well layer and a P-type layer which are stacked on the substrate in sequence. Themulti-quantum well layer comprises a plurality of quantum well layers and quantum barrier layers which grow periodically and alternately, each quantum well layer comprises a first sub-layer and a second sub-layer growing on the first sub-layer, the first sub-layer is an InGaN layer, and the second sub-layer is a Si-doped InN layer. By doping Si into the second sub-layer, the enrichment of In in the quantum well layer is facilitated, so that the spontaneous radiation intensity in the quantum well layer is increased, and the effective energy band width is increased, and accordingly the drop effect can be reduced, and the light-emitting efficiency of the diode is improved.