Watershed segmentation is suitable for producing closed region contour and providing an accurate localization of object boundary. However, it is usually prone to over-segmentation due to the noise and irregular details within the image. For the purpose of reducing over-segmentation while preserving the location of object contours, the watershed segmentation based on morphological gradient relief modification using variant structuring element (SE) is proposed. Firstly, morphological gradient relief is decomposed into multi-level according to the gradient values. Secondly, morphological closing action using variant SE is employed to each level image, where the low gradient level sets use the large SE, while the high gradient level sets use the small one. Finally, the modified gradient image is recomposed by the superposition of the closed level sets, and watershed transform to the modified gradient image is done to implement the final segmentation. Experimental results show that this method can effectively reduce the over-segmentation and preserve the location of the object contours.