Bisphenol A (BPA) has been found in aquatic environments worldwide, raising concerns about its potentially harmful effects, particularly during the early stages of organismal development. In this study, exposure to BPA significantly inhibited the development of Mytilus coruscus larvae and led to abnormal muscle development, characterized by a reduction in adductor muscle size and a decrease in the branching of velum retractor muscles. BPA exposure impaired larval metamorphosis, with reduced metamorphosis rates at 0.01 and 0.1 mu g/mL concentrations. Inhibition of velum retractor muscle degeneration and a substantial reduction in the size of adductor muscles were observed, particularly at BPA concentrations of 3 and 5 mu g/mL. BPA exposure significantly inhibited the expression of muscle growth-related genes, MHC-2560 and MHC-1792, with suppression observed at multiple stages, indicating impaired muscle development. Transcriptomic analysis showed that BPA exposure significantly affected normal physiological processes in larvae. qPCR analysis confirmed the up-regulation of genes involved in autophagy, the AMPK pathway, and detoxification, alongside the down-regulation of genes associated with apoptosis, hedgehog signaling, and neuroendocrine signaling. These findings highlight the ecological risks of BPA, as environmentally relevant concentrations disrupt critical developmental processes, including muscle degeneration during larval metamorphosis, which are essential for the survival and population dynamics of marine bivalves. BPA exposure was found to negatively impact muscle development by inhibiting the expression of genes critical for muscle growth, leading to abnormal muscle morphology. The molecular mechanisms of BPA toxicity provide important insights into its broader impact on marine ecosystems, especially during early development.