Hepatic alveolar echinococcosis (HAE), a life-threatening zoonosis, poses formidable surgical challenges when involving critical vasculature. Herein, we reported the periprocedural management dilemmas in radical resection for advanced HAE. A 58-year-old female visited the outpatient department presented with HAE. Imaging examination revealed extensive invasion of the hilum, bile duct, and several hepatic vessels, as well as left adrenal metastasis. The patient underwent right trisegmentectomy with left hepatic vein reconstruction, auto-transplantation, and adrenalectomy, with intraoperative Doppler demonstrating patent portal flow before abdominal closure. However, emergency thrombectomy and transcatheter thrombolysis were performed due to the abrupt occurrence of portal vein thrombosis 3 h after surgery. Despite intervention, the residual liver volume remained insufficient (approximately 28% of the standard liver volume), leading to progressive liver failure. The patient expired from multiorgan failure 9 days after operation. This case underscores not only the critical balance between radical resection and preservation of residual liver function in the surgical management of complex HAE, but also the imperative need to establish a comprehensive postoperative thromboprophylaxis.