Objective To explore the clinical significance of tandem mass spectrometry in neonatal genetic metabolic diseases screening in Yangzhou area. Methods The neonates in Yangzhou area between July 2017 and December 2019 were screened for genetic metabolic disorders by tandem mass spectrometry. Genetic test was offered if the screening results were suspiciously positive. Results A total of 25 771 neonates were included. Among them, 435 were positive in primary screening, 394 were recalled for retesting and 17 cases were confirmed. Among the confirmed cases, there were 10 cases of amino acid metabolism, 3 cases of organic acid metabolism, 4 cases of fatty acid oxidation metabolism and 3 cases of death. Conclusion The tandem mass spectrometry technology is widely used in the screening of amino acid metabolism, organic acid metabolism and fatty acid oxidation metabolism in neonates, which plays an important role in the early neonatal screening, diagnosis and treatment of genetic metabolic diseases.