Phthalate esters (PAEs), as a major plasticizer with multi-biotoxicity, are frequently detected in marine environments, and potentially affecting the survival of aquatic organisms. In the study, three typical PAEs (dimethyl phthalate [DMP], dibutyl phthalate [DBP] and di(2-ethylhexyl) phthalate [DEHP]) were selected to investigate the accumulation patterns and ecotoxicological effects on Mytilus coruscus (M. coruscus). In M. coruscus, the accumulation was DEHP>DBP>DMP, and the bioaccumulation in tissues was digestive glands>gills>gonads>muscles. Meanwhile, the activities of superoxide dismutase (SOD) and catalase (CAT) showed an activation-decrease-activation trend of stress, with more pronounced concentration effects. Glutathione reductase (GSH) activity was significantly increased, and its expression was more sensitive to be induced at an early stage. The metabolic profiles of the gonads, digestive glands and muscle tissues were significantly altered, and DEHP had a greater effect on the metabolic profiles of M. coruscus, with the strongest interference. PAEs stress for 7 d significantly altered the volatile components of M. coruscus, with potential implications for their nutritional value. This study provides a biochemical, metabolomic, and nutritional analysis of DMP, DBP, and DEHP toxic effects on M. coruscus from a multidimensional perspective, which provides support for ecotoxicological studies of PAEs on marine organisms.