A complex optical system used in polarization lidars often modifies the input polarization of the return signal so that it may significantly impact depolarization estimates and introduce errors to polarization lidar measurements. In most cases, retardation, depolarization, and misalignment of the system exist at the same time and interact with each other. Polarization effects of the system cannot be represented by a simple correction coefficient, so they cannot be removed using a traditional calibration method. Detailed analysis and correction technologies were provided to remove systematic biases in estimating depolarization values from a polarization lidar owing to multiple optical components. The Mueller matrices from an emitter to a receiver were calculated, and the expression for an aerosol depolarization parameter including system polarization effects was derived and obtained. In addition, the correction algorithm based on the Mueller matrix was introduced and provided. A polarization lidar was established, and the polarization characteristics of its optical components were measured with a laboratory ellipsometer; then, the Mueller matrix of the receiver was calculated and obtained. Lidar observations were performed, and our correction algorithm was applied to lidar field data. The results show that the correction method can significantly remove systematic polarization effects.