Mobile LiDAR Scanning (MLS) systems and UAV LiDAR Scanning (ULS) systems equipped with precise Global Navigation Satellite System (GNSS)/Inertial Measurement Unit (IMU) positioning units and LiDAR sensors are used at an increasing rate for the acquisition of high density and high accuracy point clouds because of their safety and efficiency. Without careful calibration of the boresight angles of the MLS systems and ULS systems, the accuracy of data acquired would degrade severely. This paper proposes an automatic boresight self-calibration method for the MLS systems and ULS systems using acquired multi-strip point clouds. The boresight angles of MLS systems and ULS systems are expressed in the direct geo-referencing equation and corrected by minimizing the misalignments between points scanned from different directions and different strips. Two datasets scanned by MLS systems and two datasets scanned by ULS systems were used to verify the proposed boresight calibration method. The experimental results show that the root mean square errors (RMSE) of misalignments between point correspondences of the four datasets after boresight calibration are 2.1 cm, 3.4 cm, 5.4 cm, and 6.1 cm, respectively, which are reduced by 59.6%, 75.4%, 78.0%, and 94.8% compared with those before boresight calibration.