Dominated by specific eco-hydrogeological backgrounds, a small watershed delineated by using the traditional method is always inauthentic in karst regions because it cannot accurately reflect the eco-hydrological process of the dual structure of the surface and subsurface. This study proposes a new method for the delineation of small watersheds based on digital elevation models (DEMs) and eco-hydrogeological principles in karst regions. This method is applied to one section of the tributary area (Sancha River) of the Yangtze River in China. By comparing the quantity, shape, superimposition, and characteristics of the internal hydrological process of a small watershed extracted by using the digital elevation model with that extracted by using the proposed method of this study, we conclude that the small karst watersheds extracted by the new method accurately reflect the hydrological process of the river basin. Furthermore, we propose that the minimum unit of the river basin in karst regions should be the watershed, whose exit is the corrosion and corrasion baselevel and a further division of watershed may cause a significant inconsistency with the true eco-hydrological process.