The relationship between the optical axes of the transmitter and the receiver of the non-coaxial lidar is affected by the external environment,such as vibration,temperature,pretightening force,etc. It leads to the geometric overlap variation of the lidar system.In further,the lidar detection accuracy and stability in far range is affected. To solve this problem, a hardware and software design of the self-alignment of geometric overlap function in the non-coaxial lidarsystem is proposed. The self-aligning system consists of a two-phase stepper motor driver, and a two-dimensional inclination adjustment platform. The laser echo signal strength is used as the correction criterion to find the best matching position of the receiving opticalaxis of the non-coaxial laser radar system. The combination of coarse scanning and fine scanning of self-alignment method is selected based on the comprehensive consideration of alignment accuracy and alignment efficiency. The coarse scan adopts the circular scanning,which can lock the transmitter optical axes within the inclination range of 0.4 mrad×0.4 mrad in 961 s. The fine scan adopts S-shaped scanning, which can achieve the inclination adjustment accuracy of 0.02 mrad in 441 s. The preliminary experiment results show that the RSCS of lidar echo signal after the self-alignment is distributed with the lidar equation, which presents an improved performance oflidar detection and can be applied for the all-day lidar measurement without man-made operation.