Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and a major cause of cancer-related mortality. In this study, the significance of NET and Contactin on the pathogenesis and prognosis of HCC was investigated, and further to explore their functions in vitro and in vivo by down regulation with siRNA. The expression of NET-1 and Contactin in HCC and in adjacent non-tumor tissues (ANT) were evaluated by immunohistochemistry, and the correlations of the expression of NET-1 and Contactin with the clinicopathological characteristics and survival of HCC patients were also analyzed. After inhibited by single-target siRNA or dual-target siRNA, the expressions of NET-1 and Contactin mRNA and protein in SMMC-7221 cells were determined by RT-PCR, Western blot and immunofluorescence stain. The cell proliferation and apoptosis were assessed by CCK-8 assays and flow cytometry (FCM). The ability of cell migration and invasion were evaluated by wound-healing migrating assay and transwell chamber assays, respectively. Subsequently, transmission system encapsulated cationic liposome was used to deliver dual-siRNA into HCC xenografts in mice. The expressions of NET-1, Cortactin, Ki67, Bax, Bcl2 and Survivin in xenograft tumor were detected by immunohistochemical staining, respectively. The positive rates of NET-1 and Cortactin in HCC tissues were significantly higher than those in ANT. In HCC, the expression of NET-1 was related to Edmondson's grade (P<0.05), cirrhosis background (P<0.001) and TNM stage (P<0.05). The expression of Cortactin was related to tumor infiltration (P<0.05), vascular invasion (P<0.001) and TNM stage (P<0.001). The expressions of NET-1 and Cortactin were positively correlated (r=0.280, P=0.004). Significant differences in the 5-year survival rates were seen between the NET-1 negative group and the positive group (P<0.05), and between the Contactin negative group (50%) and Contactin positive group (28.0%, P<0.01). The 5-year overall survival rate (OS) in NET-1 and Contactin co-expression cases (27.78%) were remarkably lower than that in both NET-1 and Contactin negative cases (54.54%) and in NET-1 positive while Contactin negative cases (47.06%, P<0.05). Univariate and multivariate Cox regression analysis revealed that NET-1 and Contactin over-expression were independent indicators for OS in HCC patients (P<0.01). There were higher expressions of NET-1 and Contactin in SMMC-7721 cells than that in other HCC cells. Dual-siRNA was demonstrated to be more effective on inhibiting cancer cell proliferation, migration and inducing apoptosis than individual siRNAs used alone in vitro and in vivo (P<0.05). The results suggest that dual-siRNA may be a great potential in siRNA-based therapeutic applications.