Brain injury, a common complication in preterm infants, includes the destruction of the key structural and functional connections of the brain and causes neurodevelopmental disorders; it has high morbidity and mortality rates. The exact mechanism underlying brain injury in preterm infants is unclear. Intestinal flora plays a vital role in brain development and the maturation of the immune system in infants; however, detailed understanding of the gut microbiota-metabolite-brain axis in preterm infants is lacking. In this review, we summarise the key mechanisms by which the intestinal microbiota contribute to neurodevelopment and brain injury in preterm infants, with special emphasis on the influence of microorganisms and their metabolites on the regulation of neurocognitive development and neurodevelopmental risks related to preterm birth, infection and neonatal necrotising enterocolitis (NEC). This review provides support for the development and application of novel therapeutic strategies, including probiotics, prebiotics, synbiotics, and faecal bacteria transplantation targeting at brain injury in preterm infants. Display omitted •The gut-microbiota-brain axis regulates vagus nerve, endocrine and immune pathways.•Preterm birth, dysbiosis and infection cause brain injury by acting on gut microbiota.•The activation of γδ T cells by the microbiome contributes to preterm brain injury.•Inflow of inflammatory cytokines across the blood-brain barrier leads to brain injury.•Metabolites of the gut microbiota may also serve as neuro-signal transmitters.