Even though the micro hole with diameter smaller than micro-meters could be made by micro-EDM process, however, the deep micro hole with high aspect ratio is a critical challenge due to the flushing problem. By conventional micro-EDM process, micro hole with the aspect ratio larger than 5~7 is still quite difficult to achieve perforations drilling. Flushing process is the key-point for deep micro hole drilling by micro-EDM. In order to improve the flushing problem, the single and dual notch cross-sectional micro tools made by WEDG technology were used for micro-EDM drilling in this study. The notch zone provides the space gap for non-flushable debris to avoid the abnormal electro-discharge generation between micro tool and work-piece. The machining characteristics of EDM drilling such as tool wear, section shape area, machining time and micro hole diameter by different cross-section micro electrode tool have been investigated in this study. The experimental results show that the single cross-sectional tools with larger notching area enhance the aspect ratio of micro hole drilling to 10 times. The roundness of tungsten carbide micro hole is approximately 0.001 mm. In the near future, it is quite possible to achieve the excellent productivity of high aspect ratio micro hole by micro EDM drilling while the notch cross-sectional micro tools are available in the commercial market.