In order to realize the fast and high accuracy alignment of Coude optical system in an alt-alt two axis tracking turntable, an auto-collimation alignment and testing system was built, which was composed of an auto-collimator with a flat reflector. The working principle and components of Coude optical system in the turntable were introduced, and its alignment and testing methods were proposed according to the principle of optical autocollimating. On the basis of the characteristics of Coude system,the principle of rectangular coordinate transformation was deduced and the fast alignment of Coude optical system was achieved with computer-aided alignment.The errors in Coude optical system with latitude and longitude axes rotated were measured. The results show that the wobble errors of Coude optical system aligned by this methods is 5.2″, which is superior to the system precision expected by laser launching system in 8″,and meets the requirements of technology index. This methods can be widely used in the alignment of Coude optical system with the two axes rotated , and has broad application prospects in practical engineering.