Abstract: In order to analyze the effect of the misalignment of crystal optical axis on the performance of a Glan-Thompson prism, the beam deflection angle, the extinction ratio and the transmittance was discussed by theoretical calculation based on the birefringence of iceland spar crystals. The theoretical calculation formulas were given. It is concluded that the misalignment of optical axis of crystal has no effect on the extinction ratio, while the misalignment of transverse direction affects the transmittance to a certain extent, and the misalignment of longitudinal direction affects the beam deflection angle. For high-precision Glan-Thompson prism, the effect of misalignment of optical axis on extinction ratio and beam deflection angle must be avoided.