Recently 3D optical microscope is developing to see micro details in three-dimensions. To see images of an optical microscope in three-dimensions, we mount two cameras on the optical microscope. Three-dimension images are created using by two images that are incoming image through the refractive mirror with eye piece lens and those are made by two cameras. In this time, because of optical design errors and deformation mechanism of an optical microscope, it makes the problem which is disconformity of images. This case cannot be made a three-dimensional image correctly. We have corrected the error-output image of 3D optical microscope and developed the system showing the correct three-dimensional image.