A monolayer closely-packed polystyrene (PS) nanosphere is prepared as mask on p-GaN substrate in the experiment. The structures of GaN nano-pillar arrays with periodic different duty ratios are prepared by changing the diameter of nanosphere mask. The experiment results show that the photoluminescence efficiency of LED of nano-pillar arrays prepared on p-GaN substrate can be raised to 3.8 times of the reference sample after normalizing power of the laser. The three-dimensional finite difference time-domain simulation shows that photoluminescence efficiency is enhanced because the periodic nano structure breaks total reflection of GaN surface, and critical angle of light output of LED structure is enlarged. In addition, we can optimize the size of nano-pillar in the same period to improve photoluminescence efficiency of LED further by changeable nanosphere mask lithography. It can be explained by effective refractive index theory and film transmittance. The theoretical and calculated results are in agreement with the experimental results.