Benzo[a]pyrene (BaP) is a representative polycyclic aromatic hydrocarbon (PAH) known for its significant toxicity and environmental persistence, capable of causing mutations, deformities, and cancer in aquatic organisms. However, systematic studies on the effects of BaP exposure on histological damage, cell apoptosis, enzyme activity changes, and gene expression in Mytilus coruscus (M. coruscus), an important ecological indicator species, remain scarce. In this study, the biological effects of BaP on M. coruscus and the immunotoxic mechanisms following BaP exposure were evaluated using histological analysis, TUNEL assay, enzyme activity assays, and transcriptome sequencing. Our findings revealed notable histopathological changes due to BaP exposure, including hemocyte infiltration, atrophy, and deformation of digestive tubules in the digestive glands, as well as epithelial cell detachment and deformation in gills. Antioxidant enzyme activities (CAT, GSH-Px, SOD, T-AOC) varied significantly across tissues under BaP stress. Additionally, significant DNA fragmentation and increased apoptosis were observed in BaP-exposed groups compared to controls. Transcriptome analysis showed that after BaP exposure, nucleotide excision repair and innate immune response pathways were suppressed, while the metabolism of xenobiotics by cytochrome P450, glutathione biosynthesis, and apoptosis pathways were upregulated. These results elucidate the toxic mechanisms of BaP on M. coruscus and the immunotoxic responses of the mussels. This study enhances our understanding of how BaP and similar pollutants affect marine bivalves, providing valuable insights for environmental monitoring and pollutant management strategies.