Objective To investigate the clinical value of three-dimensional surgery simulation system in precise hepatectomy for patients with complex liver tumor. Methods 85 patients underwent complex liver tumor resection in our hospital from May 2009 to June 2014 were retrospectively analyzed. All patients received preoperative liver CTA and then three-dimensional simulation for resected liver volume, the remnant one and surgical margin. By comparing with the actual operation data, the optimized virtual procedure for liver resection was investigated. Results The three-dimensional surgery simulation system can accurately reconstruct and display the demarcation of the tumor and its relationship with adjacent vessels. Virtual resected liver volume was statistically correlated with the actual one (P < 0.01) and the average resected volume has no difference (P = 0.068). Besides, the simulated surgical margin related to the actual margin (P < 0.01) with equal means (P = 0.256). Conclusions The three-dimensional surgery simulation system can precisely evaluate and simulate the procedure of liver surgery preoperatively, providing operation data and guidance for precise complicated tumor resection.