Vagus nerve stimulation was first used in the treatment of refractory epilepsy and depression, and its indications have expanded in recent years. The brain-gut axis is a bidirectional communication network pathway connecting the gut to the brain, maintaining homeostatic balance of the gut microbiota and shaping brain function. The vagus nerve plays an important role in brain-gut axis mechanisms in neurological disorders, which may be an important rationale for vagus nerve stimulation in the treatment of related diseases. Recent studies have shown that vagus nerve stimulation modulates the intestinal microenvironment and the intestinal microbiota, but the specific mechanisms of this alteration need further investigation. Fecal transplants or oral probiotics combined with vagus nerve stimulation may become an important therapeutic tool in the future, especially to improve the efficacy of vagus nerve stimulation for epilepsy; the gut microbiota may also be a predictive target for the efficacy of vagus nerve stimulation for epilepsy.