Accurate infrared magnetic system (AIMS) is a ground-based solar telescope with the effective aperture of 1 m. The system has complex optical path and contains multiple aspherical mirrors. Since some mirrors are anisotropic in space, parallel light undergoes complex spatial reflection after passing through the optical pupil. It is also required that part of the optical axis coincides with the mechanical rotation axis. The system is difficult to align. This article proposes two innovative alignment methods. First, a modularized alignment method is presented. Each module is individually assembled with optical reference reserved. System integration can be completed through optical reference of each module. Second, computer-aided alignment technology is adopted to achieve perfect wavefront. By perturbing the secondary mirror (M2), the influence of M2 position on the wavefront is measured and the mathematical relationship is obtained. Based on the measured wavefront data, the least squares method is used to calculate the M2 alignment and multiple adjustments have been made to M2. The final system wavefront has reached RMS=0.12 λ@632.8 nm. Through observations of stars and sunspots, it has been demonstrated that the optical system has good wavefront quality. The observed sunspot is clear with the penumbral and umbra discernible. The proposed method has been verified and provides an effective alignment solution for complex off-axis telescope with large aperture.