Random disturbance was observed in transmission intensity in various rotating prism polarizers when they were used in optical systems. As a result, the transmitted intensity exhibited cyclic significant deviation from the Malus cosine-squared law with rotation of prisms. The disturbance spoils the light quality transmitted through the polarizer thus dramatically depresses the accuracies of measurements when the prim polarizers were used in light path. A rigorous model is presented based on the solid basis of multi-beams interference, and theoretical results show good agreement with measured values and also indicate effective method for reducing the disturbance.