Objective To evaluate three dimentional (3D) reconstruction technique and methylene blue staining in precise anatomic hepatectomy. Methods The clinical data of 12 patients with hepatocellular carcinoma who were admitted to the Chinese PLA General Hospital from February 2009 to August 2011 were retrospectively analyzed. The 3D reconstruction of the liver tumor and intrahepatic vessels were done based on the computed tomography data and magnetic resonance imaging data. The portal vein supplying the tumor and its anatomic relationship with adjacent vessels were evaluated. Precise anatomic hepatectomy was performed guided by sustained methylene blue staining. Results The accurate rate of 3D model of the portal triad was 12/12. The shape of target segments observed after methylene blue staining was consistent with the Results of 3D evaluation. Two patients received hemihepatectomy, 3 received lobectomy, 5 received monosegmentectomy or subsegmentectomy, 2 received multisegmentectomy. The mean tumor diameter, operation time, blood loss, postoperative hospital stay and complication rate were 5.6 cm (2.5 16.0 cm), (150±24)minutes, (236±25)ml, (10±3)days and 2/12, respectively. After a median follow up of 14 months, tumor recurrence was found in 2 patients, and 1 of them died of tumor progression. Conclusions The 3D reconstruction may contribute to precise evaluation of the anatomic relationship between the tumor and its adjacent vessels. The 3D technique combined with sustained methylene blue staining may significantly improve the accuracy of anatomic hepatectomy.