Molluscan metabolomic analysis is essential for the understanding of the regulatory mechanism of aquatic invertebrate in response to hepatotoxic microcystins (MCs) stress. To understand the system responses of the gastropod to MC exposure, metabolomic alterations caused by two strains (MC-producing and non MC-producing) of Microcystis aeruginosa were characterized indifferent biological matrices (hepatopancreas and muscle) of Bellamya aeruginosa (Gastropoda) using 1 H nuclear magnetic resonance (NMR) spectroscopy combined with MCs detections after exposure for 1, 7, and 14 d. Although ELISA analysis showed that no MCs was detected in both tissues after non MC-producing M . aeruginosa exposure, MCs concentrations were increasing in the hepatopancreas (from 1.29±0.48 μg/g to 3.17±0.11 μg/g) and foot muscle (from 0.07±0.02 μg/g to 0.21±0.08 μg/g) after 14-d exposure of MC-producing M . aeruginosa . Meanwhile, we observed that MC induced significant increase in creatine, a variety of amino acids (leucine, isoleucine, valine, threonine, alanine, methionine, glutamate, aspartate, and lysine), carboxylic acids (lactate, acetate, and D-3-hydroxybutyrate), and choline and its derivatives (phosphocholine and glycerophosphocholine) but decreased the energy substance (lipids, glucose, and glycogen) in the hepatopancreas. However, no significant metabolite differences were observed in the muscle between MC-producing and non MC-producing cyanobacteria treated groups. These results suggest that MC exposure may cause hepatic energy expenditure accompanied with various metabolic disorders that involve lipid metabolism, protein catabolism, osmoregulation, glycolysis, glycogenolysis, and tricarboxylic acid (TCA) cycle. Moreover, metabolic perturbation was aggravated as the level of accumulated MCs raised over time in the MC-producing cyanobacteria treatment. These findings indicated that MCs accumulation might lead to oxidative-stress-mediated damage of mitochondria functions.