Both the absolute accuracy and repeatability of phase-shifting point diffraction interferometer (PS/PDI) are influenced by the alignment errors of interferometer,so a highly sensitive computer aided alignment method is necessary. A highly sensitive computer aided alignment method based on the spatial frequency domain characteristic of PS/PDI is developed. In the coarse alignment stage,the information provided by the discrete Fourier transform of the light field distribution on CCD is used to align the PS/PDI. In the fine alignment stage,the frequency domain contrast of fringes on CCD is used as the merit function to align the PS/PDI. Alignment experimental results show that the alignment repeatability of 0.1 μm can be achieved for an 1.5 μm diameter pinhole used in visible light PS/PDI.