A noise reduction signal processing method of lidar atmospheric backscattering signal with the empirical mode decomposition (EMD)is propased, and the simulation in the system is confirmed by experiment. The noise reduction algorithm based on EMD is suitable for processing of pulse signal (e.g., Block, Bump, and pulse echoing, etc.). The algorithm is used for analyzing and processing Mie lidar atmospheric backscattering signal. It shows that the noise reduction method can reduce the noise in the atmospheric backscattering signal and provide primary data of high signal-to-noise ratio (SNR) for the extinction coefficient retrieval at the next level.