Ultra-white glass is a kind of transparent low-iron glass. Owing to its excellent physical and optical properties, it is widely used in many fields such as precision electronics, luxury automobiles, and solar photovoltaic power generation. Because of its hard and brittle characteristics, the outlets of glass micro-holes are easily damaged. In order to improve the machining localization of glass micro-holes and reduce the possibility of micro-hole outlet damage, the micro electrochemical discharge drilling process was studied and optimized. Firstly, according to the principle of electrochemical discharge, the film forming mechanism and the material removal mechanism were discussed, the influence of discharge energy on the micro-holes machining technology of glass was analyzed, and an energy control model of electrochemical discharge was established. Secondly, according to the experiment, the influence of pulse voltage, frequency, and feed rate on the inlet diameter and outlet quality of the micro-holes was analyzed. Finally, the optimized parameters were chosen to fabricate a 3×3 high quality glass micro holes array with an inlet diameter of 172 μm and an outlet diameter of 167 μm on an ultra-white glass workpiece with a thickness of 300 μm; the outlets exhibited no signs of damage. The experimental results show that under the control of the discharge energy, micro electrochemical discharge drilling technology has great potential in glass micro-hole machining.