Medical image segmentation is a fundamental task in the medical imaging field. Optimal segmentation is required for the accurate judgment or appropriate clinical diagnosis. In this paper, we proposed automatically gradient threshold estimator of anisotropic diffusion for Meyer’s Watershed algorithm based optimal segmentation. The Meyer’s Watershed algorithm is the most significant for a large number of regions separations but the over segmentation is the major drawback of the Meyer’s Watershed algorithm. We are able to remove over segmentation after using anisotropic diffusion as a preprocessing step of segmentation in the Meyer’s Watershed algorithm. We used a fixed window size for dynamically gradient threshold estimation. The gradient threshold is the most important parameter of the anisotropic diffusion for image smoothing. The proposed method is able to segment medical image accurately because of obtaining the enhancement image. The introducing method demonstrates better performance without loss of any clinical information while preserving edges. Our investigated method is more efficient and effective in order to segment the region of interests in the medical images indeed.