Airborne LiDAR system is a multi-sensor integrated system, including laser scanner, global positioning system, inertial navigation system, and so on. One of the key point to obtain high positioning accuracy of laser point cloud is the airborne LiDAR calibration. And the installation angle error of laser scanner is one of the main factors which influence the measurement accuracy. Based on the working principle of airborne LiDAR system, a domestic medium range system Mars-LiDAR was developed. According to the error propagation law, the effects of measurement error and hardware installation error were analyzed. A method using different calibration field to separate installation angle errors between laser scanner and inertial navigation system was proposed. At the height of 3 000 m and 4 000 m, the high positioning accuracy was obtained, satisfying the specifications of data acquisition of airborne LiDAR. Finally the test data verified the utility, reliability and feasibility of the error calibration method by using practical engineering application.