In conventional Fourier-type magneto-optic spectrometer, the starting azimuth angle of polarizer and analyzer should be determined and aligned before the measurements. A novel method for the auto-alignment of polarizer and analyzer is proposed. The magneto-optical rotation angle can be measured and calculated without knowing the starting positions of polarizer and analyzer. The starting positions of polarizer and analyzer are computed during the measurement and can be automatically aligned. A formula of magneto-optical rotation angle error resulting from the positioning deviation of analyzer is derived, which gives a inverse proportional relation between measuring error and the square root of step number of rotating analyzer through a revolution. Numerical simulation is presented to demonstrate the theoretical analysis. As an example, the magneto-optical Kerr angle of Co films as a function of strength of magnetic field is given.