The gap control problem in hole-machining of Pyrex® wafer by electrochemical discharge machining (ECDM) to obtain a smooth quality and acceptable material removal rate is studied. Analysis of the pulse signals shows that the average current pulse interval is constant, and it is mainly related to the ion translation conditions, such as the electrolyte concentration and the flushing strategy. The most steady and intense average current density can be obtained if the voltage on-time is around 3 times the average current pulse interval and the voltage off-time is 1/4 of the on-time for bubble film dissipation. The utmost allowable feed rate at each depth is recorded as the reference of the feed rate in real continuous machining to avoid the damage to the wafer. By applying 80% of the extreme allowable feed rate, 99.9% quality-proved holes can be acquired. The diametric error at the entrance or exit is within 6%. Besides, there is no crater-like problem around the hole that facilitates the succeeding bonding process. This study contributes to the successful production of reusable optical biological chips with integrated micro fluidic channels.