Because of the complicated optic path and many optical components, relative shift of the optic mechanical parts can cause easily optic-axis parallelism departure the normal direction in high power laser launch equipment and multi-axial photoelectric tracking system. Therefore a real time auto-alignment system is proposed. Based on the alignment principle, up and down datum beam is built and paralleled with the axes of the system and the output laser separately by using the path of emitting laser. By using the CCD auto-collimator to measure the angle error of up and down path, signal is controlled to drive the fast steering mirror until the angle error of the two axes is zero. The alignment between emitting laser and the first beam expanding system and the fine alignment between the first beam expanding system and tracking and pointing system can be realized. Eperimental results show that optical-axis parallelism is 5.21″, and the accuracy of close-loop of fast steering mirror is smaller than 5＂.