Sub-wavelength photonic crystal can effectively improve the light extraction efficiency (LEE) of the light emitting diode (LED). However, it is inevitable to have defects, (namely disorder structures) during its fabrication. In this study, the LED model with ideal quadrate photonic crystal is optimized by using the finite-different time domain method. Three different LED structures with various disordered photonic crystals are further simulated. We investigate the influences of several stochastic variables (including position, radius, and depth of an air hole) of the photonic crystal on the LEE of GaN based blue LEDs. It can be found that regarding photonic crystal LED whose air hole radius is optimized to 80 nm, the stochastic variables of the position and radius will reduce its LEE. However, an opposite trend is found when this radius is replaced by 60 nm, which is not optimized. Furhermore, the LEE fluctuates inside to an extent of 53.8% as two stochastic variables (including the randomized position and the randomized radius) change from 0 nm to ±20 nm. The influence of the stochastic variables of the depth of air hole can be neglected since this variation is very small. The results in this paper have an important reference value for designing and fabricating high-performance blue light photonic crystal LED.