Unlike genetics, epigenetics involves the modification of genome without changes in DNA sequences, including DNA methylation, histone modification, chromatin remodeling and noncoding RNA regulation. MicroRNA (miRNA), a member of noncoding RNAs superfamily, participates in RNA interference through a unique mechanism. Currently, microRNAs have been found to be regulated by some natural compounds. Through altering the expression of miRNAs and influencing the downstream signaling pathways or target genes, several natural compounds exhibit its bioactivity in the prevention, diagnosis, therapy, prognosis and drug resistance of human diseases, such as cancer. In this review, several natural compounds and their studies about miRNA-related action mechanism were summarized. These studies provide a new insight into action mechanism by which natural compound exerts its bioactivity and a novel treatment strategy, demonstrating natural compound a promising remedy for clinical treatments.