As a novel class of versatile advanced materials with excellent mechanical, physical, and chemical properties, bulk metallic glasses (BMGs) are promising materials for micro-molds and micro-components. In this paper, the influence of feed rate, rotation speed, and axial depth of cut on surface roughness and top burr size of Zr41.2Ti13.8Cu12.5Ni10Be22.5 bulk metallic glass in a shear dominant zone was investigated by micro-milling with coated two-tooth cemented carbide tools. Initially, the shear dominant zone was identified by analyzing milling force, specific cutting force, surface roughness, and top burr width under different feed rates. Then, a surface morphology model considering the effect of runout was established to study the surface formation process and the influence of runout on surface roughness. Finally, the effects of rotation speed and axial depth of cut on surface roughness and burr size were investigated by an experimental approach. This study proved that, under the optimized parameters, excellent surface quality (Ra around 0.1 μm) and small burr width (below 20 μm) could be obtained by micro-milling Zr-based bulk metallic glass.