As a nontraditional processing technology, electrochemical discharge machining (ECDM) can process glass and engineering ceramics precisely. This technology has proven to be a potential process for glass 3D microstructure. However, the key to expanding the application of ECDM is how to improve machining accuracy. This research conducted micro-hole and microgroove machining. Power voltage and frequency influence on hole processing efficiency, hole entrance diameter, and hole limit depth was explored. We considered four factors affecting ECDM—the voltage and frequency of the pulse power supply, the tool electrode feed rate, and the rotation speed. We studied their influence on the roughness of the microgrooves. The results show that machining efficiency, entrance diameter, and limit depth of micro-holes increased with the increase in voltage but decreased with the increase in power frequency. The results show that the roughness of microgrooves has an apparent positive correlation with the power voltage. In contrast, it had an evident negative correlation with the power frequency and electrode speed. The bottom surface roughness of microgrooves can be as minor as 0.605 μm. Various complex 3D microstructures on the glass surface by layer-by-layer method proved the great potential of ECDM.