Processing technologies, which are required in the production of traditional Chinese medicine (TCM), has garnered attention in recent years. To address challenges associated with processed TCM and to promote its development in academia and industries, the application of metabolomics was introduced in this review, which primarily focuses on exploring TCM theories, identification of discovered compounds, and the evaluation and quality control of TCM through metabolomics. Thus metabolomics could be a powerful method for the TCM processing industry.