As the most widely used wavefront sensors in adaptive optics, Shack-Hartmann sensors can measure not only the distortions caused by atmospheric turbulence, but also the aberrations brought by mirror position errors, which are usually introduced by wind, temperature change, and mechanical stress. In this paper, we established the functional relation between the subaperture slope and misalignment based on the Shack-Hartmann sensor, and then developed a computer-aided alignment method based on the centroid deviation of lattice spots before and after optical system misalignment. This method converts the misalignment calculation into multi-objective optimization, which can be solved by multi-objective intelligence optimization algorithms. Using a three-mirror optical system as an example, the co-simulation with Python and Zemax was conducted for alignment. The simulation results show that the misalignments are reduced to the micron level after three iterations, which can meet the practical alignment requirements. The simulation results demonstrated the correctness of the proposed method.