Abstract: The SG-Ⅲ 3ω laser auto-collimation system and its control algorithm are studied based on loop feedback control theory. The operation principle, control algorithm and software control flowchart of the system are analyzed. The mathematical model for the impact of motor-control on the control result during the collimation process was established to overcome the side effects on the collimating accuracy caused by the crosstalk of both azimuth and elevation motors. By adopting the auto-collimation scheme with two-dimensional mirror mount, the collimating error converges continuously in the given precision range. The results of the test on the spot show that this SG-Ⅲ auto-collimation system meets the design specification. The SG-Ⅲ 3ω laser auto-collimation system can fulfill the collimation of 8 beams in half an hour. The angle error of the system is less than 5% for pinhole diameter per space domain, and the translation error is less than 1.0% for the accuracy of the nearfield beam diameter.