Aiming at the distorted confocal images caused by the two-dimensional scanning of MEMS galvanometer during skin imaging by reflectance confocal microscopy, the theoretical analysis of beam deflection was carried out, and the specific shape representation of projection plane scanning image was obtained. It was concluded that the theoretical distortion image was consistent with the real distortion image. The distortion mechanism was clarified and a distortion correction method was proposed. First, the original distorted grating image was recorded, then the center lines of grating were obtained based on the Hessian matrix, after that feature points were picked and datum reference lines were set. Finally, the correction to the distorted confocal images was realized by calibrating the corrections of the two-dimensional pixel distortions using polynomial interpolation based on the least square method and filling the gray value of gap pixels by weighted average method. By the experiment of measuring target with grid distortion, the correction coefficient was the highest and the root mean square error was the lowest after polynomial interpolation of degree 7. Also, the optimal number of 512 rows was 379, accounting for 74%. The residual distortions were accurately evaluated, in two dimensional, the maximum value is 4 pixels, the minimum value was 0 pixel and the average value was 1.15 pixels, so the results were accurate. The experiment of in vivo real-time skin imaging shows that the organizational structure features are more real and accurate after corrections. So this method is effective and feasible, which is helpful for accurate diagnosis of skin diseases.