The dysregulation of microRNAs (miRNAs) contributes to the pathogenesis of human malignancies, and miRNA expression can be affected by genetic and epigenetic changes, such as methylation of the CpG islands of their promoters. To identify miRNAs regulated by DNA methylation, the global miRNA expression profile was analyzed in two hepatocellular carcinoma (HCC) cell lines and two normal immortalized cell lines treated with 5-Aza-2'-deoxycytidine (DAC, an inhibitor of DNA methylation) plus TSA (Trichostatin A, histone deacetylase inhibitor). Results revealed that these epigenetic drugs differentially affect miRNA expression that is dependent or independent of cell type, especially miR-362-3p. miR-362-3p expression increased while methylation of its promoter significantly decreased in human HCC cells and tissues compared with normal cells and adjacent noncancerous tissues. Ectopic expression of miR-362-3p increased proliferation and anchorage-independent soft agar growth and its expression inhibition had opposing effects that were associated with regulation of its direct target-Tob2 in HCC cells. Inhibition of Tob2 recapitulated the effects of miR-362-3p overexpression, whereas enforced Tob2 expression reversed the promoting effects of miR-362-3p. Tob2 expression was reduced in human primary HCCs compared to adjacent noncancerous tissues. Our findings suggest that dysregulation of miR-362-3p and Tob2 may contribute to HCC malignancy.