Exposure to a poor intrauterine environment, such as maternal prenatal stress, has been linked to gut microbiota health in infants. Understanding the link between maternal prenatal bonding, early gut microbiota, and neuropsychological development may promote healthy development in early life. This study included 306 mother-child pairs. Women were assessed for maternal antenatal bonding using the Maternal Antenatal Attachment Scale in all three trimesters of pregnancy. Neonatal meconium samples were collected after birth. The behavioral temperament of infants was measured using the Very Short Form of the Infant Behavior Questionnaire–Revised at 6 months postpartum. Maternal prenatal bonding was negatively associated with the infants' relative abundance of Burkholderia and was positively associated with the relative abundance of Bifidobacterium, infant surgency and effortful control. The infant's relative abundance of Burkholderia mediates the association between maternal prenatal bonding and effortful control of the infant. This study provides new evidence about the long-term behavioral implications of a prenatally positive intrauterine environment in offspring microbiomes. The integration of maternal bonding assessment and intervention into prenatal healthcare and wellness models may modulate the establishment of gut microbiota in early life and long-term neuropsychological development in infants.