Zero order waveplates and achromatic waveplates are biplate compensators. The misalignment angle between the axes of the two waveplates affects the phase modulation of the designed compensator. A method for measuring the misalignment angle of the optical axes is reported. The method is based on a straight-through rotating-compensator system. The measurement can be implemented without the knowledge of the relative azimuthal angle between the polarizer and analyzer. The influence of the misalignment angle on the ellipsometric measurement is analyzed. The principle and mathematical expressions are given. The validation of this method is demonstrated by the simulation of measurement process. This method is valuable for inspecting and hence for improving the accuracy of biplate compensator in manufacturing.