The invention discloses a GaN-based light-emitting diode epitaxial wafer, a preparation method thereof, and a light-emitting diode, belonging to the field of epitaxy technology. The GaN-based light-emitting diode epitaxial wafer includes a substrate, and an AlN thin film buffer layer, a three-dimensional nucleation layer, a two-dimensional buffer recovery layer and an epitaxial layer stacked on the substrate in sequence. The three-dimensional nucleation layer is a GaN layer; the three-dimensional nucleation layer includes The first nucleation sublayer, the second nucleation sublayer and the third nucleation sublayer stacked on the AlN film buffer layer in sequence; wherein, the growth pressure of the first nucleation sublayer is 150-250torr, and the growth temperature is 1000-1100°C, The V / III ratio is 500‑1000; the growth pressure of the second nucleation sublayer is 500‑700torr, the growth temperature is 900‑1000°C, and the V / III ratio is 100‑200; the growth pressure of the third nucleation sublayer is 100‑ 200torr, the growth temperature is 1100-1150℃, and the V / III ratio is 200-300. By growing the nucleation layer in three sublayers to enhance the interaction of dislocations, it can finally reduce various dislocations caused by the compressive stress between the AlN film buffer layer and GaN, and improve the surface mobility of Al atoms.