The present study investigated whether quercetin mitigated fescue toxicosis-induced cardiovascular injury via the heart-gut axis. Twenty-four commercial Dorper lambs were stratified by body weight and assigned randomly to diets in one of four groups: endophyte-free without quercetin (E-,Q-), endophyte-positive without quercetin (E+,Q-), endophyte-positive plus 4 g/kg quercetin (E+,Q+) or endophyte-free plus 4 g/kg quercetin (E-,Q+) for 42 days. Body weight and average daily feed intake (ADFI) of lambs fed the endophyte-positive diets showed significant decreases. However, in the groups treated with quercetin, there were significant alterations of cardiac enzymes. Furthermore, reduced fescue toxicosis-induced histopathological lesions of heart and aorta were demonstrated in the E+,Q+ lambs. Results also suggested quercetin eased cardiovascular oxidative injury by inhibiting the increase of oxidative metabolites, and enhancing the levels of antioxidases. Quercetin reduced the inflammation response through suppressing NF-κB signaling pathway activation. Additionally, quercetin ameliorated fescue toxicosis-induced mitochondria dysfunction and improved mitochondrial quality control through enhancing PGC-1α-mediated mitochondrial biogenesis, maintaining the mitochondrial dynamics, and relieving aberrant Parkin/PINK-mediated mitophagy. Quercetin enhanced gastrointestinal microbial alpha and beta diversity, alleviated gut microbiota and microbiome derived metabolites-SCFAs dysbiosis by fescue toxicosis. These findings signified that quercetin may play a cardio-protective role via regulating the heart–gut microbiome axis.