In accordance with a three-mirror off-axis freeform system, the alignment method of combining benchmark transmission and computer-aided alignment is put forward. Based on computer-generated hologram (CGH), an entire and precise space benchmark is founded to ensure the quality of prime alignment in the process of benchmark transmission. During computer-aided alignment, by collecting interferograms of several fields of optical system by means of autocollimating interferometry, aberrations could be obtained from parameters of modified orthogonal Zernike polynomials in square area. Furthermore, the sensitivity matrices related to the incorrect parameters derived from Zemax software and those of modified orthogonal Zernike polynomials in square area are used to determine the incorrect parameters. The results show that the average root-mean-square (RMS) value of the system is 0.1641λ (λ=632.8 nm) and the average modulation transfer function (MTF) value of the system is 0.4534 after iterations.