Tumor thrombus (PVTT) is prone to be produced in the portal vein near the main tumor nodule for hepatocellular carcinoma (HCC) patients and its molecular mechanism is still unclear. In this study, we first established a HCC cell line named CSQT-01 from resected tumor thrombus in portal vein in a patient with histopathologically proved to be a moderately differentiated hepatocellular carcinoma . This cell line was composed of polygonal shaped cells and its peaks of the chromosome number was 69 and 77. Study on stem cell biology in this cell line suggests that CD133 cells represent about one fourth of the tumor cell population and CD133(+) cells possess a greater colony-forming efficiency, higher proliferative output, and greater ability to form tumor in vivo. With this cell line model and resected tumor thrombi specimen, we also studied the different expression of proteins in primary tumor and tumor thrombus and found 20 proteins expressed differentially between primary tumor and the PVTT. from these proteins, AnnexinV, Prx , CycB were selected for further analysis to find potential biomarkers of PVTT in hepatocarcinogenesis. For clinical study, we recommended a new tumor thrombus type system ( type I IV) according to anatomic features of portal vein and tumor thrombus of HCC developing modes, then evaluate this type system to predict prognosis of HCC patients. The retrospective data of 406 HCC patients with PVTT underwent resection shows that the 1y, 2y, 3y overall survival rates were 44.7 , 26.3 and 19.7 for type I, 29.9 , 20.6 and 12.4 for type II, 25.0 , 12.5 and 3.6 for type III, 27.3 , 0 and 0 for type IV, respectively, suggests tumor thrombus type system may be helpful to determine treatments and prognosis of HCC patients with PVTT.