Abstract: According to the algorithm principle of wavefront fitting and computer-aided alignment, the computer-aided alignment was realized with the damping least square method based on DDE interface technique and Zernike polynomials fitting, in which the joint calculation of MATLAB and ZEMAX is adopted. The communication between ZEMAX and MATLAB was performed through DDE interface. The visual graphical interface of basis matrix function which can generate the Zernike polynomial was written by MATLAB. The versatility and easy-to-handle characteristic of the program were implemented. The validity of the program was verified by the simulated alignment of an optical system with big obscuration ratio by using the program. In order to confirm the influence of the correlation of the Zernike circular polynomials at the annular aperture on the result of computer-aided alignment, the simulated alignment was performed by using Zernike circular polynomials and Zernike annular polynomials respectively. The simulated result shows that the two Zernike polynomials are all feasible.