In recent years, the epigenetic alterations, especially the regulation of microRNA (miRNA), have received much attention in the context of tumor development and progression. High level of oncogenic miRNAs and low expression of tumor-suppressive miRNAs are commonly observed in cancer cells. These aberrant expressions of miRNAs are intimately associated with tumor development and progression. The expression level of miRNAs could be controlled by epigenetic regulations. The hypermethylation at the promoter region of a tumor-suppressive miRNA could cause decreased expression of miRNA via the blockade of transcriptional elements. The histone modification could also indirectly cause reduced expression of tumor-suppressive miRNAs, resulting in the high expression of oncogenes. Interestingly, emerging evidences have demonstrated that several non-toxic natural agents known as nutraceuticals including isoflavone, curcumin, resveratrol, and 3,3′-diindolylmethane could significantly decrease the level of DNA hypermethylation in the promoter of miRNAs or modulate histone, leading to the alteration of miRNA expression which is believed to be associated with inhibition of tumor development and progression. Therefore, administration of these nutraceuticals combined with conventional chemotherapeutics could be a promising therapeutic strategy for fighting the war against cancers.