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Scanning Electron Microscope (SEM) is widely used in many fields to look into the nanometer world. However, there is non-linear distortion near the left boundary of high resolution images captured by SEM, which has bad effect on image processing such as image mosaic. In this paper, we propose a method to correct such distortion based on non-equidistant GM(1,1) model. We first extract pair-wise points which are the same position on target scene from two overlapped images respectively. Then the distortion is modeled using non-equidistant GM(1,1) which maps pixels of distorted image to their true positions. Finally, the corrected image is obtained with image interpolation. There is no need to pre-define the distortion model or parameters for the proposed method, and it is easy to use and flexible. Experiments show that the proposed method yields accurate correction results.