It is meaningful to study the surface morphology of monocrystalline material, but there are few studies on the surface roughness of quartz. So, surface roughness of Z-cut quartz etched by pure ammonium bifluoride and ammonium bifluoride mixed with isopropyl alcohol (IPA) solution was investigated for the first time in this paper. Firstly, when etching in pure ammonium bifluoride solutions, the surface roughness change with etching time, etching temperature, and solution concentration were studied. Then, the surface roughness improvement given by isopropyl alcohol solution was analyzed carefully. The experimental results indicated that: the surface roughness of Z-cut quartz (0001) plane increased with etching time, but decreased with etching temperature and solution concentration; the adding of isopropyl alcohol in ammonium bifluoride solution could decrease the roughness and improve the surface quality. This is the first systemic research of the evolution of quartz surface roughness when etching in ammonium bifluoride solution, and will benefit the future design and manufacture of quartz MEMS devices.