Light Detection and Ranging (LiDAR) is a technology that uses laser beams to measure ranges and generates precise 3D information about the scanned area. It is rapidly gaining popularity due to its contribution to a variety of applications such as Digital Building Model (DBM) generation, telecommunications, infrastructure monitoring, transportation corridor asset management and crash/accident scene reconstruction. To derive point clouds with high positional accuracy, estimation of mounting parameters relating the laser scanners to the onboard Global Navigation Satellite System/Inertial Navigation System (GNSS/INS) unit, i.e., the lever-arm and boresight angles, is the foremost and necessary step. This paper proposes a LiDAR system calibration strategy for a Unmanned Aerial Vehicle (UAV)-based mobile mapping system that can directly estimate the mounting parameters for spinning multi-beam laser scanners through an outdoor calibration procedure. This approach is based on the use of conjugate planar/linear features in overlapping point clouds derived from different flight lines. Designing an optimal configuration for calibration is the first and foremost step in order to ensure the most accurate estimates of mounting parameters. This is achieved by conducting a rigorous theoretical analysis of the potential impact of bias in mounting parameters of a LiDAR unit on the resultant point cloud. The dependency of the impact on the orientation of target primitives and relative flight line configuration would help in deducing the configuration that would maximize as well as decouple the impact of bias in each mounting parameter so as to ensure their accurate estimation. Finally, the proposed analysis and calibration strategy are validated by calibrating a UAV-based LiDAR system using two different datasets—one acquired with flight lines at a single flying height and the other with flight lines at two different flying heights. The calibration performance is evaluated by analyzing correlation between the estimated system parameters, the a-posteriori variance factor of the Least Squares Adjustment (LSA) procedure and the quality of fit of the adjusted point cloud to planar/linear features before and after the calibration process.