46, XY pure gonadal dysgenesis (PGD) is characterized as a female phenotype with strip-like gonads, which has a high tendency to develop into gonadal tumors. Somatic-type malignancies of germ cell tumors (SMs of GCTs) refer to the presence of malignant non-germ cell histologies admixed with GCTs, which are usually chemoresistant and indicate poor prognosis. This case report aimed to analyze the special histological type of GCTs and the importance of salvage surgery in the treatment of refractory GCTs. We report a unique case of gonadal yolk sac tumor (YST) transformed into SMs in a patient with 46, XY PGD. This 18-year-old woman underwent laparoscopic pelvic tumor resection, considered her first surgery, 2 years ago, and pathology revealed YST with initial alpha-fetoprotein (AFP) level measuring >3,000 ng/mL. She underwent seven cycles of chemotherapy, and the AFP level decreased to within a normal range after the second cycle. However, a computed tomography scan after the seventh cycle revealed abdominal and pelvic metastases, and vaginal bleeding was continuously observed. Laparoscopic exploration and laparotomy with tumor subtotal resection were performed. A pathology report showed SMs (sarcoma) derived from YST. Whole exome sequencing demonstrated that the main somatic mutation was a non-synonymous mutation of KRAS (c.182A>G), and this result did not show any indications for targeted drugs. She received three cycles of PEI (cisplatin, etoposide, and ifosfamide) chemotherapy but showed no response. She refused to undergo further treatment and has been alive with the disease for 7 months. This suggests that SMs may be one of the reasons for chemoresistance of refractory GCTs, and salvage surgery may be one of the most effective treatments for this patient. Targeted therapy may be a new choice for chemoresistant GCTs, but drug selection must be based on gene sequencing, and its efficacy still needs to be verified by further study.