The analytical study on transmitted intensity′s perturbance of the Glan-Taylor prism with varying rotation angle is given. It is found that the variation of the transmitted intensity with the rotation angle deviates from Malus law, exhibiting a cyclic fluctuation with the rotation angle. The occurrence of the disturbance is explained by interferance between the monochromatic light passing through the Glan-Taylor prism and the factor of the crystal-air interface transmissivity, which together lead to the relation between the transmitted intensity and the incident angle. The notion of the perturbance factor is introduced, and the influences of the factor discussed systematically. Theoretical results meet well with the experiment. Effective measures for weakening the disturbance are presented. The discussions here supply theoretical basis for the design,production and use of the polarizing prisms.