As a nontraditional processing technology, Electrochemical discharge machining (ECDM) can precisely process glass and engineering ceramics. 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. The influence of power voltage and frequency on hole processing efficiency, hole entrance diameter and hole limit depth 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 obvious positive correlation with the power voltage, while it had an obvious negative correlation with the power frequency and the electrode speed. The bottom surface roughness of microgrooves can be as small as 0.605µm. Various complex 3D microstructures on the glass surface by layer-by-layer method, which proved the great potential of ECDM.