When the slope stability is calculated, it is usually simplified to two-dimensional plane strain problem. The limit equilibrium method is used to calculate the safety factor after two-dimensional slicing of the main section. Obviously, it is a simplified model of the reality of a slope, although the phenomenon of slope failure occurred in the three-dimensional space. Strictly, a three-dimensional slope stability analysis should be performed. The paper provides a three-dimensional micro-column method which has expanded the traditional two-dimensional slice method and built the three-dimensional slope model based on high-resolution DEM. In this method, the soil slices in two-dimensional slice method have accordingly transformed the soil columns. Lastly, through analyzing the force condition of every column, based on the limit equilibrium theory, three-dimensional Bishop method is imbedded into GIS software platform by secondary development mode, and the three-dimensional spherical sliding surface is constructed and the three-dimensional factor of safety is calculated. The method realizes the automation and integration of 3-D model construction and 3-D safety factor calculation process, and expands the application of high-resolution DEM in geotechnical engineering field.