The aligning between the punch and die governs no only the burr formation characteristics but also the life time of the punch and die in the sheet metal blanking process. There are many ways to adjust the two elements in the general punching systems but in the case of micro punch system, the punch size is reduced to a few tenth of micrometer range and the general aligning methods are almost impossible to apply. The image processing is the most widely used method in micro punch aligning, but in order to apply the method, it needs quite a large space for visionary system to approach the punch-die aligning zone. In this paper, the new punch-die aligning method with using the total capacitance between the punch and die hole is proposed. In this method, the tip surface of the punch tool locates at the same plane of the die surface and the capacitance variation between the two elements are measured. When the center of the two elements are coincided, the capacitance is minimized, but when the align is changed to any direction, the capacitance between the two elements increase. In order to verify the feasibility of this method, the aligning and punching tests was performed.