High-purity quartz (SiO2) is an important material widely used in many industries, including semiconductor technology, telecommunication, and optics. The content and distribution of impurities in quartz significantly affect the processing methods. This paper provides an insightful review on the processing of high-purity quartz, covering the analytical techniques, separation methods, and the critical procedures used to assess the quality of quartz ore. More importantly, the critical review of the thermal phase transition separation method for fine-grained mineral inclusions, micron-grade fluid inclusions, and lattice-bound trace elements is notably opened for the first time. It is proposed that the research field as a monopolized industry would benefit by expounding the critical problems that occur during the preparation of high-purity quartz.