In this paper, the high performance GaN-based light-emitting diodes (LEDs) on carbon-nanotube-patterned sapphire substrate (CNPSS) by metal-organic chemical vapor deposition (MOCVD) are demonstrated. By studying the mechanism of nucleation, we analyze the reasons of the crystal quality improvement induced by carbon nanotubes (CNTs) in different growth process. Combining with low temperatures photoluminescence (PL) measurements and two-dimensional (2D) finite difference time-domain (FDTD) simulation results, we conclude that the improvement of optical properties and electrical properties of CNPSS mainly originates from the improvement of the internal quantum efficiency (IQE) due to decreased dislocation density during nano-epitaxial growth on CNPSS. Additionally, in order to reduce the light absorption characteristics of CNTs, different time annealing under the oxygen environment is carried out to remove part of CNTs. Under 350 mA current injections, the light output power (LOP) of CNPSS-LED annealed 2 h and 10 h exhibit 11% and 6% enhancement, respectively, compared to that of the CNPSS-LED without annealing. Therefore, high temperature annealing can effectively remove parts of CNTs and further increase the LOP, while overlong annealing time has caused degradation of the quantum well resulting in the attenuation of optical power.