In order to improve the light emitting efficiency(LEE) of GaN-based blue LED, two LED models covered by ZnO nano-structures, including nano-rod and nano-cone structures, are simulated in the method of FDTD. The results of these simulations show that the light emitting efficiency of LED is varying regularly with the different nanostructures’geometric parameters (such as the period: P, the wide of bottom: W, and the length: L). The optimized model structure is obtained, and it is found that both ZnO nano-rod and nano-cone can bring obviously incensement (250% and 230%) on LEE. Besides, with the analysis on the variation curve, the influence of ZnO nano-structure and the reason of the optimization results are theoretically explained. These results provide a theoretical reference on the practical design and optimization of highly efficient GaN-based LED.