The treatment of central nervous system disorders remains a clinical challenge, highlighting an urgent need for innovative therapeutic strategies. The gut-brain axis represents a complex bidirectional communication network between the gastrointestinal tract and the brain, with the vagus nerve serving as a critical pathway for signal transmission. Vagus nerve stimulation (VNS), an established therapy for drug-resistant epilepsy and depression, has been shown to modulate the composition and functional output of gut microbiota, which in turn influences disease progression. Concurrently, gut microbiota and their metabolites such as short-chain fatty acids can regulate vagal activity through feedback mechanisms. This bidirectional interaction operates through neural, immune and metabolic pathways. This review provides a systematic review of the mechanisms through which VNS influences gut microbiota, and how microbial products feedback to regulate vagus nerve activity and the integrated pathways underlying this cross-talk, for the sake of providing insights into novel therapeutic approaches targeting the gut-brain interface.