A separated Sagnac interferometer with optical diameter of 60 mm and spectral channel of 65 is introduced based on its working principle. Ideal interference fringes and interference fringes are simulated when reflector has an angle deviation, and the effect of alignment error to the interference fringes is analyzed. The position accuracy and angle accuracy of alignment are induced based on the optical design parameters. The method of precision alignment is introduced in detail, which includes the installation of primary alignment plane, the precise location of splitting prism, the precise adjustment of long-arm and short-arm reflectors. Through the installation of alignment refrence and the masterly refrence transformation, the precise alignment of separated Sagnac interferometer is achieved based on the principle of auto-collimation, whose position accuracy is better than 0.01 mm, angle accuracy is better than 1″, super possition accuracy of primary working plane is better than 1″.