Quartz is a widely used material in the field of microelectromechanical systems (MEMS) for fabricating devices such as substrates, probes, and lenses; it is also indispensable as a resonator or oscillator for frequency control in communication and network technologies. However, its development is limited because it is difficult to fabricate an ideal profile for implementation in complex structures. In practice, wet etching is the most effective and extensive method for achieving the expected structure, although dry etching and other special machining techniques have also been investigated. In this study, the dynamic wet etching process was recorded using different ratios of buffered oxide etcher (BOE) solutions as the etchant to reveal the etching mechanism. The experiments were first designed considering the fabrication of samples, experimental conditions, and measurement indicators. Subsequently, the corresponding etch rate, roughness, and surface morphology were investigated to control the process parameters during wet etching. Different etchants exhibit varying etching rates and roughness properties. A smaller proportion of hydrofluoric acid in the BOE solution results in lower etch rate, and vice versa. The roughness (Ra) in the stable stage was not completely consistent with the tendency of the etch rate, whereas the surface morphology and dimensions of the pyramids rationally complied with the roughness trend. Additionally, the results suggested that the three following stages exist during the wet etching process of the z-cut α-quartz wafer; smooth, incremental, and stable. The analysis of the dynamic wet etching process in this study is beneficial for the structural design, manufacturing, and performance of quartz MEMS devices.