Objective To explore the clinical features and molecular diagnosis of 46, XY disorder of sex development (46, XY DSD). Methods The clinic data of one child with 46, XY DSD raised as female were retrospectively analyzed, and related literatures were reviewed. Results The 11.5-year-old child raised as female visited clinic due to, “accidently found clitoral hypertrophy for half month”. Preliminary series of laboratory examinations supported the diagnosis of 46, XY DSD, high gonadal hormone dysplasia. DNA sequencing of the whole genome exon group showed a heterozygous mutation of c.937C ＞ T, p.Arg313Cys in NR5A1 gene. No abnormality was detected in her father, while her mother was a heterozygous mutation carrier. Conclusions 46, XY DSD can be diagnosed by the whole genome exon gene sequencing.