Stress birefringence resulted from the growth defect of YAG crystal is tested and analyzed using the photoelastic stress theory. Combined with the test result, the effect of the stress birefringence on the conversion efficiency of large aperture multi-disks YAG laser is calculated. The result indicates that it causes 36.3% wasting in average where stress exists, which is a spatial modulated function, in the range of 0～0.9997. The static transmission rate and the near field spot distribution are measured in the experiment and validate the calculation.