Objective To compare the effect of two chemotherapeutic patterns after hepatectomy of hepatocellular carcinoma （HCC） with portal vein tumor thrombi（PVTT）. Methods The clinical data of 51 HCC patients with PVTT who were treated in our department from June 2006 to December 2011 were analyzed retrospectively. Fifty-one HCC patients with PVTT who were performed hepatectomy and treatment of antivirus and improve immune were divided into two groups according to chemotherapeutic patterns after operation： portal vein infusion drug deliver system （PVIDDS）group （n=19） and transcatheter arterial chemoembolization（TACE） group（n=32），and to compare the treatment effect of the two groups. Results The recurrence rate of 1-month, 1-year，3-year， and 5-year after operation in TACE group was 3.1%（1/32），46.9%（15/32），84.4%（27/32）， and 100%（32/32），respectively. And in PVIDDS group, which was 5.3%（1/19），52.6%（10/19），100%（19/19）， and 100%（19/19），respectively. There were no differences in recurrence rate of 1-month, 1-year, and 5-year after operation in two groups（P＞0.05）. Recurrence rate of 3-year after operation in TACE group was lower than that in PVIDDS group（P＜0.05）. There were no differences in medial survival time（17.1 months vs.15.9 months）， survival rate of 1-year（93.8% vs.94.7%） and 3-year（40.6% vs. 36.8%） after operation in TACE group and PVIDDS group（P＞0.05）. Survival rate of 5-year after operation in TACE group was higher than that in PVIDDS group（21.9% vs.0, P＜0.05）. The rate of complication in TACE group was lower than that in PVIDDS group（65.6% vs.94.7%，P＜0.05）. Conclusions If the HCC patients with PVTT could endure operation，surgical resection should be considered firstly，furthermore antivirus treatment, improving immune，and chemotherapy should be considered after operation. The effect of TACE is better than PVIDDS.