Objective To investigate the incidence of fatty acid oxidative metabolism disorders (FAOD) in the neonatal population in ethnic minority areas of Hainan Province, and to analyse the clinical characteristics of the diagnosed children, so as to provide the basis for the prevention of birth defects in Hainan Province. Methods Tandem mass spectrometry screening data of newborns with inherited metabolic disorders from October 2016 to December 2021 were collected from ethnic minority areas in Hainan Province. Tandem mass spectrometry was used to detect the levels of free carnitine as well as 30 acylcarnitines in dried blood spots of newborns. Initial screen-positive neonates were recalled for review of blood tandem mass spectrometry, urinary organic acids were measured by gas-phase mass spectrometry, and peripheral blood was collected from neonates and their parents for gene sequencing. Results A total of 46285 newborn samples were screened, of which 513 were positive in the first screening, the positive rate of the first screening was 1/90, 501 cases were recalled, and 11 cases of fatty acid β -oxidation metabolic disease were diagnosed, the incidence rate was 1/4208, including 6 cases of primary carnitine deficiency, 1 case of short chain, medium chain and very long acyl-CoA dehydrogenase deficiency, and 1 case of carnitine palmitoyl transferase I and II deficiency. Conclusion The incidence of fatty acid β-oxidative metabolic disease is high among newborns in minority areas of Hainan province, and primary carnitine deficiency is more common. It is suggested that the screening of neonatal genetic metabolic diseases by tandem mass spectrometry should be included in the routine of newborn screening program.