Taking advantage of good hermeticity, tiny parasitic capacitance, batch mode fabrication, and compatibility with multiple bonding techniques, the glass-silicon composite substrate manufactured by the glass reflow process has great potential to achieve 3D wafer-level packaging for high performance. However, the difference in etching characteristics between silicon and glass inevitably leads to the formation of the undesired micro-protrusions near the silicon-glass interface when preparing a shallow cavity etched around a few microns in the composite substrate. The micro-protrusions have a comparable height with the depth of the cavity, which increases the risks of damages to sensitive structures and may even trigger electrical breakdown, resulting in thorough device failure. In this paper, we studied the characteristics of the chemical composition and etching mechanisms at the interface carefully and proposed the corresponding optimized solutions that utilized plasma accumulation at the interface to accelerate etching and bridge the gap in etching rates between different chemical compositions. Finally, a smooth transition of 131.1 nm was achieved at the interface, obtaining an ideal etching cavity surface and experimentally demonstrating the feasibility of our proposal. The micromachining solution is beneficial for improving the yield and structural design flexibility of higher performance micro-electromechanical systems (MEMS) devices.