The quality of Chinese medicines (CMs) is the basis to guarantee the clinical safety, effectiveness, and controllability of medicinal materials. It is the lifeline to promoting sustainable development of the CM industry. The research and application of quality evaluation methods is a national strategic issue related to the scientific and industrial development of CMs. Recent progress in computational methods and high throughput technologies makes it possible to comprehend CM molecular and systematic levels. Especially in recent years, a new era of omics has emerged, opening an exciting and fertile area to investigate the holistic change and quality evaluation of CMs. This review summarizes the current research advances of omics in the quality evaluation of CMs and concludes with an outlook on future trends and opportunities for omics research in CMs. In particular, the role of omics according to different factors affecting the quality of CMs, such as origin, medicinal part, producing area, cultivation pattern, harvest time, growth stage, and processing method, have been highlighted. This review would lay a foundation for the accurate evaluation of CM quality and further improve the quality standards of CMs.