In order to improve the light extraction efficiency of light-emitting diode (LED), according to the equivalent medium theory, microstructure array with frustum of a cone is designed and fabricated in the LED passivation layer (SiNx) surface. The influence of the fill factor of the bottom surface, bottom diameter, height and angle of the micro structure on the light extraction efficiency of LED is emphatically analyzed through simulation.to improve light extraction efficiency of LED. The results show that when the micro structure of the fill factor of the bottom surface is 0.55, the radius of bottom surface is 220 nm, the height is 245 nm, and the side slope angle is 70°, the light extraction efficiency of the device is optimized. Which is 4.85 times as much as the device without surface micro structure. The sub-wavelength nanostructure is prepared on the surface of LED passivation layer by nanosphere lithography technology, and the comparison test of electroluminescent between the proposed structure and LED chip without surface micro structure is carried out. The results show that the luminous efficiency of the samples with micro structure at 20 mA and 150 mA working current are 4.41 times and 4.36 times of the reference samples without micro structure. The calculated results and the experimental results are consistent, which means that the structure produced by the LED passivation layer can effectively improve the light extraction efficiency.