Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is a rare autosomal recessive inborn error of mitochondrial fatty acid oxidation. It is caused by rare mutations as well as polymorphic susceptibility variants. We describe here the case of a 1-year-old male patient who had growth and mental retardation, seizures, and recurring fever since infancy. Urinary gas chromatography/mass spectrometry (GC/MS) showed elevated levels of ethylmalonic acid. Plasma acylcarnitines on tandem mass spectrometry (MS/MS) and elevations of C4-cartinitine are consistently present. The two polymorphic susceptibility variants of the short-chain acyl-CoA dehydrogenase (SCAD) gene, c.625G>A and c.322G>A, were detected. Because of its highly variable clinical characteristics, there are no related reports in China. This report broadens the phenotype and genotype of SCADD in China and underlines the difficulty of diagnosis.