Microplastics (MPs) are prevalent throughout the oceans and pose a significant global environmental concern due to their detrimental effects on various living organisms. While researchers have investigated the toxicity mechanisms of MPs in marine species, there is a need for a more comprehensive understanding, particularly regarding the potential adverse effects on the growth and metabolism of bivalves. In this study, indoor exposure experiments were conducted on Pinctada fucata martensii to examine the impact of commercial polyvinyl chloride (PVC)-MPs (50 μm, 15 mg/L). The aim was to determine the effects of MPs on the hepatopancreas metabolism of P. f. martensii. Non-targeted metabolomics analysis indicated alterations in the hepatopancreatic metabolic of P. f. martensii following exposure to PVC-MPs. A total of 32, 27, and 154 differential metabolites (SDM) were identified in EG (1-d) vs CG (1-d), EG (15-d) vs CG (15-d), and EG (1-d) vs EG (15-d), respectively (VIP >1 and P < 0.05). Further examination of metabolic pathways revealed that PVC-MPs disrupted the metabolism of amino acids, particularly alanine, aspartic acid, and glutamic acid metabolism; this suggests that the organism may have developed neurotoxicity. Sphingolipid metabolites showed a significant up-regulation in both EG (15-d) vs CG (15-d), as well as in EG (1-d) vs EG (15-d), indicating lipid peroxidation in the hepatopancreas of P. f. martensii following PVC-MPs exposure. Additionally, in EG (1-d) vs CG (1-d), starch and sucrose metabolism were significantly inhibited, glycolysis or gluconeogenesis pathways were promoted, and changes in energy metabolism were promoted. This study sheds light on the impact of MPs on the metabolism of bivalves, offering fresh insights into the detrimental effects of MPs on aquatic organisms.