Retinoic acid functions through two classes of receptors, i.e., the retinoic acid receptor (RAR) and the retinoid X receptor (RXR). The difference in the role between RAR and RXR, however, are not well clarified. In the present study, we comparatively investigated the phenotypic and global gene expression changes in Xenopus tropicalis embryos induced by three different agonists, including a RAR selective ligand (all-trans retinoic acid, at-RA), a RXR selective ligand (fluorobexarotene, FBA) and their common ligand (9-cis retinoic acid, 9c-RA). All three agonists induced striking and similar malformations in X. tropicalis embryos at the concentrations of 5–50 μg/L. Especially, the development of anterior structures and caudal region was dramatically altered. The hierarchical clustering analysis of phenotypes and gene profiles suggested that effects induced by 9c-RA separated from those by at-RA and FBA. The up-regulated genes were involved in multiple pathways while down-regulated genes were mainly related to phototransduction and tyrosine metabolism. at-RA primarily affected the retinol, glycolysis, starch and sucrose metabolisms while FBA led to disturbances in more wide-ranging pathways such as the PPAR, adipocytokine, insulin, FoxO signaling pathways, alanine, aspartate and glutamate metabolism. RXR is a heterodimeric partner for several other nuclear receptors, which opens the possibility that additional retinoid effects could be mediated by FBA, such as RXR-PPAR. Our data indicates that not only RXR-RAR but also RXR-PPAR plays important roles in the control of metabolism with retinoid treatment in X. tropicalis embryos.