Surface morphology obtained using micro electrical discharge machining (micro EDM) not only provides important information, such as wear and lubrication properties, but also shows many micro peaks and craters, which are very different from that machined using traditional methods. Hence, surface morphology evaluations in micro EDM processes using traditional evaluation parameters are not appropriate. In this study, a novel evaluation method, which includes a wavelet lter and the fractal theory, was proposed and analyzed in detail to evaluate the surface morphology in order to achieve the required precision and concision. First, a novel evaluation method was proposed, and the effectiveness of the method was investigated. Second, a series of relevant experiments based on titanium alloys and high-speed steels were conducted to validate the effectiveness of the new method, the analysis results were presented. Third, the fractal trend in the surface morphology was summarized based on the titanium alloy and high-speed steel materials; the rules governing the relationship between the fractal dimension and the surface morphology were proposed. Finally, the phenomena observed in the analysis process were investigated and discussed in detail.