The automatic alignment of resonator is one of the critical techniques in high-power laser technology. The method of computer-aided alignment of unstable resonator is presented and its numerical simulation results are given. The relation between mirror misalignments and its phase aberration coefficients is regarded as linear to some extent, especially under the condition of small misalignments. After getting a series of aberrations representing a misaligned system, we get the data of each misalignment by solving linear equations. Then the misaligned resonator is modified according to these results. The whole process is simulated numerically. Presently, multi-misalignments including both tilt and decentration can be calculated in this way. The numerical analysis shows that it is easy to figure out a single misalignment. Complex misaligned condition needs iteration. Tilt misalignments that can be figured out is 10～104 μrad and the decentration range is 10-2～1 mm. This method can be used to guide resonator′s alignment effectively and provide another way for laser resonator’s automatic alignment in practical use.