According to principle of lidar and experiences, the automatic alignment system of lidar beam controlled by computer procedure has been designed. By controlling the position of gimbal-mounted mirror, the direction of light beam scanning was east-west and south-north. Echo signals were analyzed, and final position was obtained to make transmitting and receiving systems parallel. The process needs 10-20 min for once, and accuracy is about 0.1 mrad. In atmospheric temperture monitoring, measuring results compared with CIRA86 data. The error of altitude at 30-45 km is 1-3 K, 2-5 K for 45-65 km.