In order to get high-resolution glomerulus image with large field of view (FOV), stitching multiple small FOV images with high-resolution is necessary. Directly stitching images without properly correction is not acceptable and cannot afford any significant assistance in pathological diagnosis for intensity inhomogeneity and geometric distortion. Therefore we proposed a method of distortion correction and intensity inhomogeneity correction of glomerulus transmission electron microscope (TEM) image. In this paper, we firstly describe how these two distortions degrade images. Secondly, based on the TEM imaging system, image acquisition model and distortion correction model were proposed. Then according to these two models, distortions were greatly degraded and stitching results were improved by respectively applying two corrections, intensity inhomogeneity correction and geometric distortion correction. With the method proposed here, the result was improved significantly and stripes, fuzzy and artifacts were decreased dramatically. Our method has been proved to be valid to solve the problems of TEM glomerulus image distortion and at the same time to improve the result of multiple TEM glomerulus image stitching.