We demonstrated the formation of GaN-based nanorod (NR) structure by using self-assemble Ni nanoislands as the etching mask. It was found that crystal quality of the GaN epilayer prepared on an NR GaN template was significantly better than that prepared with a conventional low-temperature GaN nucleation layer. With the NR GaN template, it was found that 20-mA light-emitting diode (LED) output power can be enhanced by 39.8%, as compared to the conventional LED.