Objective To analyze the screening status and genetic variation characteristics of primary carnitine deficiency (PCD) in neonates in Hefei. Methods A total of 631839 newborn screening samples screened by Hefei Neonatal Disease Screening Center from January 2016 to December 2021 were detected by tandem mass spectrometry. Newborns and their mothers with positive initial screening were recalled for re-screening. If the re-screening results were still lower than the critical reference value, high-throughput second-generation gene sequencing was performed. Results A total of 32 neonates were diagnosed with PCD (overall incidence: 1/19745). Among 32 neonates, 31 underwent high-throughput sequencing combined with Sanger validation, 1 had no genetic variation and 30 had genetic variation (18 boys and 12 girls). There were 25 cases of complex heterozygous variation and 5 cases of homozygous variation, and the gene diagnosis rate was 96.8%. Among the 60 variants of SLC22A5 gene in 30 positive children, c.1400C>G had the highest variation ratio, accounting for 48.3% (29/60), followed by c.51C>G, accounting for 15.0% (9/60). Conclusions The overall incidence of neonatal PCD in Hefei was not significantly different from that in other areas of China. c.1400C>G and c.51C>G were the common sites of PCD gene variation in newborns in Hefei City.