Evidence is emerging of a tight link between cardiomyocyte autophagy and cardiac hypertrophy (CH). Sustained exposure to stress leads CH to progress to heart failure. Several miRNAs have been described in heart failure, and miRNA-based therapeutic approaches are being pursued. Although microRNA-365 (miR-365) has been testified as a positive modulator of CH, the specific mechanism remains unclear. In the present study, we observed that miR-365 expression was up-regulated in hypertrophic cardiomyocytes both in vivo and in vitro, and was accompanied by dysregulation of autophagy. We found that miR-365 negatively modulates autophagy in hypertrophic cardiomyocytes by targeting Skp2. Overexpression of Skp2 promoted autophagy and rescued CH induced by Ang-II; conversely, Skp2 knockdown further inhibited autophagy and CH. Furthermore, we found that the activation of mammalian target of rapamycin (mTOR) signaling was regulated by Skp2 following Ang-II treatment, as indicated by the up-regulation of p-S6K and p-4EBP1 levels. The inactivation of mTOR by rapamycin completely abolished the Ang-II-induced inhibition of autophagy. In conclusion, our study provides substantial evidence that miR-365 and its target gene Skp2 play a functional role in CH and suggests the development of novel therapeutic options based on miR-365 and Skp2.