Objective To analyze the clinical features of neonatal enterovirus infection and to explore the effect of antibiotic management improvement on reducing the use of antibiotics in children with enterovirus infection. Methods A retrospective analysis was performed on the clinical data of neonates diagnosed with enterovirus infection who were admitted to the Neonatal Department between January 2019 and December 2023. The subjects were categorized into a general infection group and a severe infection group based on the presence or absence of organ failure, and comparative analyses of clinical characteristics between the two groups were conducted. Results A total of 153 neonates with enterovirus infection were included in the study, with the peak incidence occurring from May to July. There were 94 boys and 59 girls. The gestational age was 39.3 (38.1-40.3) weeks, and the birth weight was 3200.0 (2950.0-3450.0) g. There were 35 early neonates, and the age of onset was 15.0 (8.0-23.0) days. Among all the patients, 146 had the initial symptoms of fever, 152 had fever during the course of the disease, and the course of fever was 1.8 (1.5-2.4) days. The median white blood cell count at admission was 5.0 (3.5-7.2)×10⁹/L and the median C-reactive protein level was 2.4 (0.5-7.3) mg/L. The median procalcitonin level was 0.2 (0.1-0.3) ng/mL. All 146 patients in the general infection group were discharged after improvement. Among the 7 patients with severe infection, 4 were complicated with hemorrhagic hepatitis syndrome and 2 died; 3 patients were complicated with myocarditis and 2 died. Compared with the general infection group, the infants in the severe infection group had a lower gestational age, a higher proportion of poor appetite and poor reaction during the course of the disease, lower hemoglobin and platelet counts, higher levels of lactic acid, aspartate aminotransferase, alanine aminotransferase, creatine kinase, and creatine kinase MB isoenzyme, with statistically significant differences (P<0.05). A total of 9 serotypes were detected in PCR positive samples of enterovirus, among which Coxsackie virus B3, Echovirus 12 and Echovirus 30 were the most common, accounting for 62.7%. After the implementation of antibiotic management quality improvement, the utilization rate of antibiotics was lower in neonates with enterovirus infection, and the duration of antibiotic use and hospital stay were shorter, and the differences were statistically significant (P<0.05). Conclusions The neonatal enterovirus infection is mainly mild, but the mortality of severe infection is high. There are some differences in the laboratory results between mild and severe patients. Enterovirus PCR, sequencing typing and antibiotic management improvement measures are helpful for reasonable diagnosis and treatment.