The signal-to-noise ratio (SNR) of an atmospheric lidar decreases rapidly as range increases, so that maintaining high accuracy when retrieving lidar data at the far end is difficult. To avoid this problem, many de-noising algorithms have been developed; in particular, an effective de-noising algorithm has been proposed to simultaneously retrieve lidar data and obtain a de-noised signal by combining the ensemble Kalman filter (EnKF) and the Fernald method. This algorithm enhances the retrieval accuracy and effective measure range of a lidar based on the Fernald method, but sometimes leads to a shift (bias) in the near range as a result of the over-smoothing caused by the EnKF. This study proposes a new scheme that avoids this phenomenon using a particle filter (PF) instead of the EnKF in the de-noising algorithm. Synthetic experiments show that the PF performs better than the EnKF and Fernald methods. The root mean square error of PF are 52.55% and 38.14% of that of the Fernald and EnKF methods, and PF increases the SNR by 44.36% and 11.57% of that of the Fernald and EnKF methods, respectively. For experiments with real signals, the relative bias of the EnKF is 5.72%, which is reduced to 2.15% by the PF in the near range. Furthermore, the suppression impact on the random noise in the far range is also made significant via the PF. An extensive application of the PF method can be useful in determining the local and global properties of aerosols.