This article reported a male neonate with Smith-Lemli-Opitz syndrome (SLOS) caused by DHCR7 gene compound heterozygous variations. The patient presented with multiple malformations and feeding difficulties after birth and was transferred to the First Affiliated Hospital of Hunan Normal University (Hunan Provincial People's Hospital) from a local hospital eight days later. Physical examination found general scleredema, scalp defects, short penis, urinary tract malformation, bilateral syndactyly of the second and third toes, and low serum cholesterol. Whole-exome and Sanger sequencing indicated a compound heterozygous mutation in the DHCR7 gene, c.852C>A(p.F284L), and a de novo mutation of c.820_825del(p.N274_V275del). SLOS is rare in the Asian populations and prone to missed diagnosis and misdiagnosis with difficulty in clinical management. The possibility of SLOS should be considered for newborns with multiple malformations and low serum cholesterol.