Objective To summarize the methods, safety, and efficacy of the ex vivo liver resection followed by autotransplantation in the treatment of advanced hepatic alveolar echinococcosis (HAE). Method A retrospective analysis of clinical data and follow-up data in 21 cases who received ex vivo liver resection followed by autotransplantation in the treatment of HAE from February 2014 to December 2016 in West China Hospital was performed. Results All the patients successfully underwent ex vivo liver resection followed by autotransplantation and no death happened during operation. The median weight of remnant liver was 701.4 g (360–1 300 g), the average operation time were 13.6 h (9.4–19.5 h), the anhepatic phase time were 180–455 min with median of 314 min. The average of intraoperative blood loss were 2 379 mL (1 200–6 000 mL). The average of patients entered red blood cell suspension were 10.6 u (0–39.5 u), the average of fresh frozen plasma were 1 377 mL (0–6 050 mL) , of which 7 patients received autologous blood transfusion, with average of 1 578 mL (500–3 700 mL). The average of postoperative hospital stay were 23.5 days (4–51 days). Postoperative complications occurred in 12 patients during hospitalization, and 4 cases of postoperative complications were in grade Clavien-Dindo Ⅲ or above, 2 cases of grade Ⅴ (died). During the follow-up period, 19 patients were followed for a median of 16.2 months (3–38 months), no HAE recurrence or metastasis was found, only 1 patient were lost follow-up after surgery for 12 months. Massive ascites and hyponatremia were found in 1 patient who was diagnosis as left hepatic vein stenosis at the end of the 3 months after operation. The patient was cured after interventional treatment of hepatic vein stent implantation and angioplasty. Conclusions The ex vivo liver resection followed by autotransplantation provides radical treatment for patients with advanced HAE, but the surgery is difficult and has high risk of postoperative complications. The detailed preoperative evaluation, intraoperative pipeline reconstruction reasonably, and fine postoperative management can improve the patient’s survival, and reduce the rate of complications.