As a huge micro-ecological system of the human body，intestinal flora is closely related to the occurrence and development of many diseases. Acupuncture and moxibustion are important methods to treat diseases，and their regulation of intestinal flora has attracted more and more attention. Clinical and animal experiments have confirmed that acupuncture treatment can regulate the intestinal flora to become balanced. This paper compiled the development of research methods on intestinal flora in recent years as well as the influence of acupuncture on gastrointestinal diseases and metabolic diseases，and looked ahead to the problems and development direction of the research of acupuncture intervention in intestinal flora.