Objective To explore feasibility and safety of ex vivo liver resection and autotransplantation in treating end-stage hepatic alveolar echinococcosis combined with secondary cavernous transformation of portal vein. Methods The patient was diagnosed with the end-stage hepatic alveolar echinococcosis combined with secondary cavernous transformation of portal vein. The ultrasonography, computed tomography, and magnetic resonance imaging were used to access the characteristics of the lesions and the extent of involvement of the portal vein and its branches. The liver model was reconstructed using a three-dimensional imaging data analysis system (EDDA Technology, Inc. USA), the remnant liver volume and the extent of involvement of the first hepatic hilum were recorded. Then the multidisciplinary team repetitively discussed the risks and procedures involved in the surgery. Finally, the ex vivo liver resection and autotransplantation was proposed. Results The preoperative evaluation showed the patient had a large intrahepatic lesion which severely invaded the retrohepatic inferior vena cava, the right hepatic vein, and the middle hepatic vein and were completely occluded, the left hepatic vein was partially invaded, and the portal vein was spongiform. The remnant liver volume was 912 mL, the ratio of residual liver volume to standard liver volume was 0.81. The preoperative liver function Child-Pugh score was grade A. The ex vivo liver resection and autotransplantation was successfully managed according to the expected schedule. The autografts (made by patient’s great saphenous vein) were used to reconstruct the hepatic vein and portal vein, and the retrohepatic inferior vena cava was not reconstructed. The patient recovered well and was discharged on day 20 after the operation. Conclusions Ex vivo liver resection and autotransplantation could successfully be applied in treating patient with end-stage hepatic alveolar echinococcosis combined with secondary cavernous transformation of portal vein. Adequate preoperative assessment and management of the first hepatic hilum are key to this operation.