This paper analyzes the misalignment causes of modulation depth in the Infrared Fourier Transform Spectrometer (IFTS). Then, an automatic adjustment algorithm (AAS) is presented accordingly. The AAS includes three steps: coarse adjustment, precise adjustment and high precise adjustment. The maximum modulation is searched by two step motors in two dimensions. The experimental results show that this AAS is able to adjust the modulation misalignment in the IFTS automatically.