Traditional Chinese medicine (TCM), an essential component of the traditional medicine practiced in China, has demonstrated unique therapeutic efficacy in combating infectious diseases caused by pathogens and various types of tumors. In particular, TCM plays a vital role in enhancing immune function, maintaining homeostasis, and improving metabolic balance. However, the complex ingredients used in TCM and its broad range of therapeutic targets present challenges for comprehensive analysis of the mechanisms involved. Moreover, the molecular and cellular mechanisms underlying TCM's effects remain underexplored, limiting its broader application in modern medicine. Recent studies have increasingly revealed that TCM can not only directly inhibit the activity of pathogens, such as bacteria, fungi, viruses, and tumor cells, but also exert profound effects on immune remodeling by regulating the metabolism of both pathogens and hosts. Therefore, a comprehensive understanding of the role of TCM in metabolic regulation is crucial for elucidating its anti-pathogenic effects. This review is focused on the metabolic pathways of pathogens and host metabolic reprogramming induced by pathogens. We systematically reviewed the mechanisms by which TCM regulates pathogen metabolism, influences pathogen-induced metabolic reprogramming in hosts, and mitigates immune suppression caused by pathogens. This review may provide new ideas for investigating the molecular mechanisms of TCM in disease development and progression.