Our main aim was to evaluate the value of medical image three-dimensional visualization system (MI-3DVS) in pancreaticoduodenctomy patients with hepatic artery variance. 114 patients who had undergone pancreatoduodenectomy were retrospectively summarized and analyzed. Clinical data of 64-slice multidetector CT angiography (64-MDCTA) scanning was introduced into MI-3DVS for procedural segmentation, registration and 3-dimensional (3D) reconstruction. The findings were compared with those found during the operation and by postoperative digital subtraction angiography (DSA) of coeliac artery. The 3D model demonstrated the origination and bifurcations of blood vessels, and the relationships among neoplasms, organs and blood vessels efficiently. About (14/114 cases, 12.3%) had variant. The sensitivity, specificity and accuracy of MI-3DVS in variant hepatic artery diagnosis were 100%. It assisted in preoperative procedural planning that was consistent with intraoperative findings. MI-3DVS can be applied for accurate diagnosis of hepatic artery variance. It also provides detailed preoperative guidance for individualized procedural planning.