Active imaging technology can perceive the surrounding environment and obtain three-dimensional information of the target. Among them, light detection and ranging (LiDAR) imaging systems are one of the hottest topics in the field of photoelectric active imaging. Due to the small size, fast scanning speed, low power consumption, low price and strong anti-interference, a micro-electro-mechanical system (MEMS) based micro-scanning LiDAR is widely used in LiDAR imaging systems. However, the imaging point cloud will be distorted, which affects the accurate acquisition of target information. Therefore, in this article, we analyzed the causes of distortion initially, and then introduced a novel coordinate correction method, which can correct the point cloud distortion of the micro-scanning LiDAR system based on MEMS. We implemented our coordinate correction method in a two-dimensional MEMS LiDAR system to verify the feasibility. Experiments show that the point cloud distortion is basically corrected and the distortion is reduced by almost 72.5%. This method can provide an effective reference for the correction of point cloud distortion.