This study presents the development of a drilling technique for an innovative tabletop drilling machine that combines micro-EDM with drilling to fabricate micro-holes in diamond-tool. The mechanisms designs of double V-shaped bearings and double spindles which provide a precision clamping and vertical alignment for diamond-tool and micro-tube are devised to enable to machine a co-centric micro-hole for micro-tool. A diamond-tool, made with copper-based sintered alloy, is drilled by using the developed technique of co-centric micro-hole EDM-drilling into a hollow shaft which can create equilibrium of drilling forces, prevent a drilling squeezing to be occurred and enable to offer a temporary storing space for drilling chips. Relative experiments including the determinations of drilling ratio and discharge capacitance are carried out via this established machine. Experimental results show that excellent geometric and dimensional accuracy of micro-holes on the diamond-tool can be achieved.