Background Newborn screening (NBS) is a public health service aimed at identifying infants with severe genetic disorders. Genetic testing is now commonly used for secondary or confirmatory testing after a positive result in some NBS programs. Recently, next-generation sequencing (NGS) has emerged as a robust tool that enables large panels of genes to be scanned together rapidly. Rapid advances in NGS emphasize the potential for genomic sequencing to improve NBS programs. Neonatal genetic screening represents a critical advancement within contemporary NBS frameworks, integrating NGS to enhance disease detection sensitivity and specificity. Materials and methods This study, conducted through multicenter collaboration in Changsha, screened 2019 neonatal samples for 75 common genetic disorders involving 135 pathogenic genes. The aim was to explore the incidence and mutation spectrum of these disorders in the Chinese population and to propose an optimized screening model. Results The results showed a positive detection rate of 0.74% and a carrier rate of 31.50%. Conclusion This study provides valuable data for refining neonatal genetic screening protocols in China.