Objective To analyze the results of genetic metabolic disease screening and gene mutation characteristics in newborns in Haikou, Hainan. Methods A retrospective analysis was conducted on 185 660 newborns born at the Haikou Maternal and Child Health Hospital from March 2017 to March 2021 who underwent genetic metabolic disease screening. All newborns underwent tandem mass spectrometry screening for genetic metabolic diseases within 7 days after birth. The positivity rate of genetic metabolic disease screening in newborns was statistically analyzed, and the specific gene mutation characteristics of the metabolic diseases were investigated. Results Among 185 660 newborns in Haikou, 88 were diagnosed with genetic metabolic diseases, with a total prevalence rate of 1 in 2 110 (47.40 per 100 000). Among the 88 cases, the prevalence rates of organic acidemia, amino acid metabolism disorders, and fatty acid oxidation disorders were 1/3 640, 1/10 921, and 1/9 283, respectively, with methylmalonic acidemia, medium-chain acyl-CoA dehydrogenase deficiency, and citrin deficiency ranking the top three.Genetic testing revealed that in 42 cases of methylmalonic acidemia, MUT and MMACHC mutation genes were detected, with the c.609G>A mutation in the MMACHC gene being the most common（37.97%）. The ACADM mutation genes in 15 cases of medium-chain acyl-CoA dehydrogenase deficiency were mainly detected at c.387+1delG (25.00%), c.449_452delCTGA(16.67%), and c.1076C>T (16.67%). The SLC25A13 mutations in 8 cases of citrin deficiency were mainly detected at c.154C>T(37.50%) and c.1638_1660dup (25.00%). Other detected mutation genes in genetic metabolic diseases mostly had 2 or 1 mutation sites. During treatment and follow-up, 49 children were normal (55.68%), 36 children experienced developmental delays(40.90%), and 3 children died (3.41%). Conclusion Haikou, Hainan has a certain incidence of genetic metabolic diseases in newborns, with medium-chain acyl-CoA dehydrogenase deficiency, methylmalonic acidemia, and citrin deficiency having the highest prevalence. These diseases exhibit specific characteristics in mutation sites.