Self-standing ZnO nanotube (ZNT) arrays were fabricated on the surface of a GaN-based emitter with an indium tin oxide (ITO) transparent layer using a hydrothermal method and temperature cooling down process. For the greater enhancement of photon extraction efficiency, ZNT/SiO core-shell nanostructure arrays were fabricated on the emitter with a 430 nm wavelength. The optical output power of ZNT/SiO core-shell arrays on the emitter with ITO electrode was remarkably enhanced by 18.5%, 28.1%, and 55.9%, compared to those of ZNTs, ZNRs on an ITO film on an emitter and ITO film on an emitter as a conventional emitter, respectively. The large enhancement in optical output is attributable to the synergistic effect of efficient photon injection from the ITO/GaN layer to ZNTs because of the well-matched refractive indices and wave-guiding, in addition to the superior photon extraction by the SiO coating layer on the ZNTs.