A 73-year-old man with a history of heterotaxy syndrome and intestinal malrotation developed hemorrhagic shock due to bleeding from a duodenal ulcer. Esophagogastroduodenoscopy failed to achieve hemostasis because of restriction of the view by massive hemorrhage. Transcatheter arterial embolization cannot achieve endovascular hemostasis due to the vascular anatomy. Therefore, surgical hemostasis was achieved. Intestinal malrotation due to heterotaxy syndrome is a risk factor for gastrointestinal bleeding. Severe gastrointestinal bleeding in patients with intestinal malrotation is difficult to control with endoscopy alone. Therefore, combined therapies with endoscopy, interventional radiology, surgical procedures, and intensive care are vital for achieving a better prognosis.