This study aimed to evaluate the efficacy of arterial infusion of 5-fluorouracil (5-FU) combined with subcutaneous injection of pegylated interferon alpha-2b (PEG-IFNα-2b) on unresectable HCC with PVTT and to determine the potential survival benefits of patients from this therapy. From January 2007 to August 2009, HCC patients with PVTT were assigned to undergo arterial infusion of 5-FU with subcutaneous injection of PEG-IFNα-2b or palliative therapy. A total of 105 HCC patients (94 males and 11 females) aged 24-78 years with portal vein thrombosis were randomly assigned to 5-FU/PEG-IFNα-2b group (n = 55) or control group (n = 50). The median progression-free survival (PFS) was 10 months, and the median overall survival (OS) was 12 months for all patients. The 6- and 12-month OS rates were significantly higher in 5-FU/PEG-IFNα-2b group than in control group (81.04 vs. 22.72%, 48.03 vs. 0%, both P < 0.05). The median OS and PFS were significantly longer in 5-FU/PEG-IFNα-2b group than in control group (14.7 vs. 4.5 months, 12.5 vs. 9 months, both P < 0.05). For unresectable HCC with PVTT, arterial infusion of 5-FU combined with subcutaneous injection of PEG-IFNα-2b reduces tumor size obviously, prolongs patient survival, and causes no severe adverse events.