Objective　To investigate the clinical, biochemical and genetic features of a Chinese boy with holocarboxylase synthetase deficiency (HCSD). Methods　The clinical and genetic data of a rare case of HCSD were retrospectively analyzed. Results　After birth, the boy showed development delay. At 3 months old, the boy was started with rehabilitation. Tandem mass spectrum and gas chromatography analysis was carried in the 5th month after birth because of the recurrent upper respiratory tract infection and elevated level of C5-OH in the blood and decreased level of C0，and elevated level of 3-OH-propionic, pyruvic acid, methylcrotonylglycine in the urine were in accordance with the HCSD. Genetic analysis found compound heterozygous mutations of c.1648G>A and c.1544G>A in gene, of which the latter one is novel. After the treatment of biotin (20 mg/d) and L-Carnitine, the condition of this boy was gradually improved. Conclutions　HCSD is characterized with slow onset and inconspicuous manifestations. The confirmed diagnosis can be built with MS/MS, GC/MS analysis and gene mutation analysis. The effect of early biotin treatment is satisfactory. In this study，we carried out clinical and genetic diagnosis，which lays a solid foundation for prenatal diagnosis and early treatment.