To realize the fast, efficient alignment of off-axis three-mirror anastigmatic(TMA) system, a computer aided alignment(CAA) method was proposed. First, the aberration characteristics in the misaligned off-axis TMA system was theoretically analyzed to determine the evaluation parameters in CAA. Second, the key alignment parameters to be adjusted were given by combining the misalignment characteristics with the actual situation of the optical assembly. Finally, the magnitudes and orientation of the alignment parameters were calculated with the measurement data and CAA model. In order to verify the method, an off-axis TMA system was aligned according to this CAA method. The wave-front error (WFE) of the center and extreme edge FOVs were measured by wave-front sensor. After only once calculation and alignment, the measured root mean square (RMS) WFEs were reduced from 0.32λ to 0.067λ(λ＝632.8 nm). The experiment results demonstrate that this CAA method is feasible.