An analytical study on transmitted intensity perturbance of Glan-Thompson prism with varying rotation angle is given, when the linearly polarized light enters in the normal incidence. The perturbance strongly affects the quality of transmitted polarizing light. In order to reduce this bad effect and hold the quality of transmitted polarized light, we reaserched the perturbance factor. Study shows that the transmitted intensity sensitively relies on the incident angle. In the experiment,a minute random variation of the incident angle around the structure angle of Glan-Thompson prism is found, which gaves rise to the perturbance. Selecting the right angle could reduce the perturbance. For the same purpose,we should reduce the thickness of the glue in certain wavelength to the full and select the hump at the average temperature when the temperature varied.