【Objective】 To investigate the clinical characteristics and molecular genetic mechanism of 46,XY complete gonadal dysplasia (46,XY CGD) caused by a new mutation of NR5A1 gene. 【Methods】 The clinical data of a female patient with 46 XY karyotype were retrospectively analyzed, and the whole exon group and mitochondrial group genes were detected. 【Results】 The clitoris was hypertrophic. The patient had both urethral orifice and vaginal orifice, and there was no common passage between them. Ultrasonography showed an unclear primordial uterus and bilateral ovaries. The gonad biopsy showed poorly developed testicular tissue. Karyotype was 46,XY. The detection of whole exon group and mitochondrial group genes indicated a new heterozygous missense mutation in NR5A1 gene on chromosome 9, and the variation information was c.205C>T:p. Arg69Cys. The mother did not carry the gene mutation. 【Conclusion】 The clinical manifestations of 46,XY CGD are diverse. NR5A1 gene mutation is one of the important causes, which provides a basis for the clinical diagnosis and pathogenesis of the disease.