Gas electron multipliers (GEMs) have been widely used for particle collection and signal amplification. Because of the advantages of glass, such as high hardness, aging resistance, and dielectric strength, research into its application as a substrate material in GEM design and process has attracted extensive attention in recent years. This paper compares two commonly used glass GEM structural designs and shows that the optical transparency of the hexagonal symmetric structure is superior to that of the rectangle structure. An electric field model is developed to characterize the negative correlation between the hole diameter and the electric field strength. The structure of glass GEM is designed according to the feasibility of the process. A new process method of surface metal patterning using hole filling to form a mask is proposed, which can meet the high alignment and shaping requirements of the perfect match between the opening of metal layer and the aperture shape of the substrate. Combined with the advanced laser hole modification process, a glass GEM sample with a hole diameter of 70 μm, a spacing of 140 μm, a substrate thickness of 240 μm, and a metal thickness of 13 μm is obtained. Finally, particle trajectories, avalanche region coverage, and electron energy are discussed based on the prototype structure.