46, XX male syndrome is a rare disorder of sex development. One-tenth of 46, XX male syndrome is sex-determining region Y (SRY)-negative. We used whole-exome sequencing (WES) analysis associated genes to investigate the underlying genetic etiology of 46, XX male syndrome patients with bone marrow failure with a typical male phenotype. WES reveals SRY and SRY-box family genes were negative. Simultaneously, gene variants were detected in female pathway, testis development, and steroid receptor genes. There are undefined gene variants associated with congenital bone marrow failure. WES proved an efficient diagnostic method toward 46, XX male syndrome patients with hematological disorder.