Acupuncture has a good curative effect in the treatment of gastrointestinal system diseases, such as functional dyspepsia, ulcerative colitis, and constipation. The central nuclei which are involved in the mechanism of acupuncture in regulating the gastrointestinal system have become a research hotspot in recent years. In the present paper, the authors summarized the effect of acupuncture and the central nervous system on gastrointestinal function regulation. It was found that the regulation of gastrointestinal function by acupuncture involved many brain regions such as the amygdala, paraventricular nucleus, locus coeruleus, raphe nucleus, and dorsal nucleus of the vagus nerve. Of these, the limbic brain region had the closest relation. However, the included studies were animal experiments, which involved less research on nuclear group interactions. The role of central nuclei in the regulation of gastrointestinal function by acupuncture is unclear. Thus, the introduction of more advanced brain imaging techniques to observe brain dysfunction of central nuclei and the relativity of acupuncture in regulating gastrointestinal function will be the focus in the future study, which will contribute to determining the effective mechanism of acupuncture and moxibustion.