Water eutrophication leads to the frequent occurrence of cyanobacterial blooms, which pose a serious threat to the health and survival of fish, the top consumer in freshwater ecosystems. The hepatotoxicity induced by microcystin-LR (MC-LR) has been well studied; however, its impact on the intestinal flora and the gut-liver axis has rarely been reported. This study aimed to investigate the harmful effects of acute oral (303.89 µg/kg.bw) and intraperitoneal (i.p., 101.3 µg/kg.bw) exposure to MC-LR on the intestine and liver and the gut-liver axis of common carp. The results showed that the transaminase activity and levels of proinflammatory factors increased significantly, and histological abnormalities were observed, indicating that MC-LR induced a hepatoenteric inflammatory response. The levels of gram-negative bacteria increased, but the expression levels of bile acid (BA)-related genes (cyp7a1, cyp8b1, cyp27a1, and fxr) and the short-chain fatty acid (SCFA) content decreased as the LPS level increased. These results suggest that MC-LR exposure induces liver inflammation and impairs BA synthesis, weakening intestinal defences and promoting LPS-related hepatic inflammation. Additionally, increased intestinal permeability and reduced SCFA synthesis can further compromise intestinal epithelium protection. The inflammation induced by MC-LR was significantly more severe in the liver than in the intestine, and the recovery of the liver was slower. This study enhances the understanding of the environmental risks posed by cyanobacteria.