Abstract: The activity and expression of drug metabolizing enzymes and transporters changes significantly under high altitude hypoxia. The gut microbiota is an important factor affecting the metabolism of drugs through direct and indirect actions, changing the bioavailability, biological activity or toxicity of drugs and affecting the efficacy and safety of drugs. High altitude hypoxia significantly changes the structure and diversity of the gut microbiota, which may play a role in drug metabolism. This article reviews the effects of high-altitude hypoxia on the gut microbiota and the effects these changes on drug metabolism.