Objective To investigate the incidence, etiological classification, clinical features and prognosis of neonatal hyperammonemia through a retrospective multi-center status survey. Methods Neonatal patients with blood ammonia levels more than 100 μmol/L who were treated in 28 participating units between January 2017 and November 2022 made up the study population. The incidence, etiological classification, clinical traits, genetic phenotype, and prognostic follow-up of neonates with confirmed hyperammonemia were analyzed using descriptive study methodologies. Results During the observation period, the total number of deliveries in 28 units was 708421, and 73 newborns met the diagnostic criteria of neonatal hyperammonemia, including 44 boys and 29 girls. The etiological classification included congenital hyperammonemia (24 cases, 32.88%), transient hyperammonemia (11 cases, 15.07%), secondary hyperammonemia (12 cases, 16.44%), and unexplained hyperammonemia (26 cases, 35.61%). The main clinical manifestations were poor response, shortness of breath, feeding difficulties, convulsions and impaired consciousness. The main abnormal laboratory tests were metabolic acidosis, increased blood lactate, hypoglycemia, electrolyte disorders, abnormal blood and/or urine amino acids. Genetic tests were performed in 13 patients, and abnormalities were found in 11 of them. In addition to conventional symptomatic supportive treatment, arginine intravenous drip (21 cases), carnitine supplementation (8 cases), blood purification (9 cases) and peritoneal dialysis (3 cases) were mainly used. The prognosis for the 24 cases of congenital hereditary hyperammonemia was 10 deaths, 6 treatment discontinuations, and 8 discharges. Among the 12 children with secondary hyperammonemia, 1 died, 3 gave up treatment, 1 had an unknown prognosis, and 7 were cured and discharged from hospital. All 11 cases of temporary hyperammonemia were cured or improved and discharged from hospital. Among 26 cases of unknown hyperammonemia, 17 died, 4 gave up treatment, 3 had unknown prognosis, and 2 were discharged from hospital after improvement. Conclusions Neonatal hyperammonemia is uncommon, but it progresses swiftly and has a high risk of mortality, particularly in cases of congenital genetic hyperammonemia and unexplained hyperammonemia. Raising doctors' awareness of the condition and promoting early detection and treatment can reduce mortality and serious consequences. Moreover, setting up screening and registration procedures for newborn hyperammonemia as well as improving prenatal consultation are helpful for clinical outcomes.