Wavefront detection is the main technical means of enhancing telescope alignment. Due to the limited internal space for the large aperture optical system, we propose a computer-aided alignment method based on eigenmode coefficients to solve misalignments in telescopes. Compared with the traditional sensitivity matrix method, in the proposed method, the amount of calculation is small, the detector does not need to be partitioned, and the structure of the wavefront reconstruction matrix is simplified. We analyze the relationship between the eigenmode coefficient and the misalignment of the secondary mirror, and establish a sensitivity matrix model between the two. The alignment of the 1-m aperture on-axis three-mirror telescope was simulated. In the misalignment range of decenter ±0.3 mm and the tilt ±0.2° for the secondary mirror, an aberration correction was achieved in two-step iteration, and the root-mean-square of the central field wavefront aberration was less than λ/14, which has a good practical value for the alignment of large aperture optical systems in the future.