The Wnt/JNK pathway, responsible for tissue polarity in cardiogenesis in vertebrates, has been shown to play numerous roles during differentiation and development of cardiac myocytes. Van Gogh-like-2 (Vangl2) is a core component that regulates the induction of polarized cellular and tissue morphology during animal development. However, little is known about Wnt/JNK signaling pathway in the process of myocardial remodeling. In present study, we found that activation of Wnt/JNK signaling by Wnt5a stimulates enlargement of cardiomyocyte surface area. The hypertrophic features were inhibited in Vangl2 depleted cells. Meanwhile, Wnt/JNK activation induced cytoskeleton rearrangement but failed to activate these effects in cells lacking Vangl2. Moreover, Wnt/JNK activation significantly increased the cell apoptosis by mediating the mitochondrial permeability transition pore (mPTP) dysfunction, whereas knockdown of Vangl2 partly reversed these effects. These results suggest that activation of Wnt/JNK signaling stimulates myocardial remodeling (cell morphological changes, apoptosis and mitochondrial dysfunction), in which Vangl2 may play an essential role.