Determine the misalignment of optical element quickly and exactly is the key to the technology of computer-aided alignment (CAA). For alignment a three-mirror off-axis field bias system, the sensitivity matrix method was used to simulate the alignment process. The results of simulation show that the sensitivity matrix method was not convergence. A new CAA method to get misalignment was put forward; the misalignment was obtained by programming the function of optical design software CODE V's auto-optimization option. The system's alignment characteristic was analysis and made use of this new method put up a computer simulation. The results of simulation show that the misalignment determined by only once auto-optimization and guidable to alignment of this system. After alignment, the optical system produced a measured wave front error across the all image plane less than 0.08 waves RMS at λ=0.6328μm.