Objective To explore the relationship between amniotic fluid meconium contamination (MSAF) and intrauterine hypoxia, neonatal asphyxia and clinical indexes of vaginal delivery. Methods 80 neonates with amniotic fluid meconium contamination (MSAF) who delivered vaginally from June 2021 to June 2024 in the neonatal department of our hospital were retrospectively collected and included in the MSAF group. In addition, 126 cases of vaginal delivery neonates who were excluded from amniotic fluid meconium contamination due to high risk factors of infection were selected as the non-contaminated group. Baseline data were collected and compared between the two groups. Intrauterine hypoxia, neonatal asphyxia, MSAF fecal contamination, fetal heart monitoring, ultrasound examination and laboratory indicators were detected. Neonatal and maternal outcomes of the two groups were analyzed and compared. Fetal heart monitoring and laboratory indicators of intrauterine hypoxia and non-intrauterine hypoxia in MSAF group were compared. The results of ultrasonic examination and laboratory examination in different degrees of neonatal asphyxia in MSAF group were compared. Results The total labor duration of MSAF group was significantly longer than that of the non-contaminated group, the 1min Apgar score of newborns was significantly lower than that of non-contaminated group, postpartum hemorrhage, intrauterine hypoxia, neonatal asphyxia and NICU occupancy rate were significantly higher than those of non-contaminated group (P < 0.05). The proportion of MSL, the proportion of unresponsive fetal heart monitoring and the level of ox-LDL in serum in intrauterine hypoxia group were significantly higher than those in non-intrauterine hypoxia group (P < 0.05). In MSAF group, there were 10 cases of mild neonatal asphyxia, 5 cases of severe neonatal asphyxia and 65 cases of non-neonatal asphyxia. The MSL ratio, S/D value, blood lactic acid, CK-MB and TBA levels in severe asphyxia group were significantly higher than those in mild asphyxia group and non-neonatal asphyxia group (P < 0.05), and the S/D value, blood lactic acid, CK-MB and TBA levels in mild asphyxia group were significantly higher than those in non-neonatal asphyxia group (P < 0.05). Conclusion The incidence of intrauterine anoxia and neonatal asphyxia is high in women with MSAF during vaginal delivery. The exposure time of MSAF should be shortened as far as possible to detect and prevent the occurrence of serious complications.