The topography errors of micro electrical discharge machining (micro-EDM) surface are mainly composed of surface roughness, surface waveness and profile error. These three errors influence the workpieces functions and performances in varying degrees. Thus, how to pick up these compositions without distortion is very important for surface comprehensive topography evaluation. In this paper, the roughness of micro-EDM surface contour lines is separated by wavelet method. Firstly, it is certified that any curve line could be indicated by different frequency parts with multi-resolution analysis, which is the feasibility study for roughness separation with wavelet method. Then, the mathematical model of roughness separation of contour lines is set up. Finally, the formula of roughness separation times with wavelet theory is given.