The invention provides a GaN-based light-emitting diode epitaxial wafer and a preparation method thereof, the GaN-based light-emitting diode epitaxial wafer comprises a multi-quantum well layer, and the multi-quantum well layer is of a periodic structure formed by alternately stacking quantum well layers, quantum well cap layers and quantum barrier layers; the quantum well cap layer comprises a BInGaN sub-layer, a composite sub-layer and a BGaN sub-layer which are stacked in sequence, the composite sub-layer is of a periodic structure formed by alternately stacking SiN layers and BN layers, the growth temperature gradient of the BInGaN sub-layer, the growth temperature gradient of the composite sub-layer and the growth temperature gradient of the BGaN sub-layer are increased, and the In component content of the BInGaN sub-layer is gradually reduced. The cap layer in the multi-quantum well layer is specially designed, so that the aim of protecting the In component of the quantum well is well fulfilled, well-barrier lattice mismatch is reduced, In segregation at a quantum well-barrier interface is relieved, the interface crystal quality at the quantum well-barrier is improved, the well-barrier interface is steeper, and the performance of the device is improved. The improvement of wavelength uniformity and the acquisition of better antistatic capability are facilitated, and the luminous efficiency of the light-emitting diode is successfully improved.