Although veno-arterial extracorporeal membrane oxygenation (VA-ECMO) has been used to aid myocardial recovery in patients with postcardiotomy cardiogenic shock (PCCS), it has been associated with adverse effects. The combined use of VA-ECMO and Impella (ECPELLA) for PCCS, however, has been reported to be efficacious with few reports of thromboembolic events. We present a case of aortic thrombosis with visceral malperfusion during ECPELLA management for PCCS. We performed the Bentall procedure, mitral valve repair, tricuspid annuloplasty, and coronary artery bypass graft on a 73-year-old man admitted with congestive heart failure caused by annuloaortic ectasia, along with severe aortic and mitral regurgitation. VA-ECMO and Impella were required, since the cardiopulmonary bypass weaning was difficult. Impella was removed on postoperative day 4. On postoperative days 5 and 6, laboratory data showed worsening renal dysfunction, lactate levels, and acidosis. Contrast-enhanced computed tomography showed thrombosis in the celiac and superior mesenteric arteries. Aortic thrombectomy was performed. Hyperkalemia, caused by a reperfusion injury, resulted in ventricular fibrillation. Continuous hemodiafiltration improved the hyperkalemia. However, irreversible acidosis progressed, and the VA-ECMO flow rate could not be sustained. On postoperative day 7, the patient died. Perioperative use of Impella for PCCS may be effective in improving postoperative cardiac function. When sudden organ failure is observed after surgery, it is necessary to not only keep the exacerbation of cardiogenic shock in mind, but also the possibility of thrombosis.