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Objective To establish a monitoring system and a standard database system for neonatal hearing screening program and evaluate its effect. Methods The hearing screening data of newborns in Nanjing in 2021 from the neonatal hearing screening information system of Jiangsu Province were selected as the experimental group, and the manual registration data of neonatal hearing screening in Nanjing in 2020 were selected as the control group. The initial screening rate, re-screening rate, referral rate and hearing impairment disease management rate of neonates were compared between two groups. Results The initial screening rate, re-screening rate and referral rate of neonatal hearing screening in the information management system were 99.27%,85.73% and 91.60% respectively, which were significantly higher than those in the manual registration control group (96.94%, 68.36% and 66.20%, P<0.05).Conclusion The application of neonatal hearing screening information system can greatly improve the efficiency of neonatal hearing screening, improve the referral rate and the management ability of intervention and follow-up for children diagnosed with hearing impairment, and contribute to the establishment of prevention and control health management system.