We have theoretically studied the transmission intensity disturbance in the spinning Lippich prism polarizer. Experimental results indicate that the variation of the transmission intensity with the rotation angle deviates from Malus’ cosine-squared law and exhibits stochastic fluctuations. We first consider the effect of the discontinuous rotation of the polarizer. Then we study the effect of the stochastic vibration of the polarizer in the direction perpendicular to the rotation direction based on the multi-beams interference theory. The numerical result confirms that the latter contributes majorly to the disturbance. Further studies show that the magnitude of the disturbace depends sensitively on the cement material of the polarizer, and it can be reduced to rather low levels when appropriate material is selected.