The anti-cancer role of miR-206 in hepatocellular carcinoma (HCC) cells has been reported, but its mechanism of action remains poorly understood. This research aimed to investigate the anti-HCC mechanism of miR-206. We analyzed 25 pairs of HCC and adjacent tissue specimens from HCC patients. Two patient-derived HCC cell lines were established. MiR-206 levels in tissue specimens and cell lines were detected by qRT-PCR. MiR-206 overexpression was mimicked by miR-206 mimic transfection. MET or CTNNB1 gene was overexpressed by transient transfection. Protein and protein phosphorylation levels of interests were assessed by western blotting. HCC cell malignancy in vitro was evaluated by cell proliferation, apoptosis, colony formation, trans-well invasion assays as well as western blotting assessing the marker proteins of epithelial or mesenchymal phenotype. We found that miR-206 level was significantly lower in HCC tissue specimens in comparison to adjacent counterparts. Two patient-derived HCC cell lines showed lower miR-206 level than L02 human hepatocytes. MiR-206 mimic transfection significantly reduced phosphorylation levels of pan-Akt Ser9, Erk1 Thr202/Tyr204 and Gsk-3beta Ser308 as well as protein levels of beta-catenin and c-Met in primary HCC cells in vitro. Luciferase reported assay and AGO2-RNA co-immunoprecipitation assays results demonstrated that miR-206 reduced MET and CTNNB1 gene expressions in HCC cells by interacting with the 3′ UTR of their mRNAs. Restoring c-Met or beta-catenin protein level by MET or CTNNB1 transient overexpression partially restored the malignancy of HCC cells in vitro. We concluded that miR-206 might inhibit HCC development by targeting MET and CTNNB1 gene expression.