Per- and polyfluoroalkyl substances (PFASs), including perfluorooctane sulfonate (PFOS) and its alternative 6:2 chlorinated polyfluoroalkyl ether sulfonate (F53B), are widely used in industries, leading to their presence in aquatic environments and potential adverse effects on marine organisms, particularly during early development. This study investigates the effects of PFOS and F53B on larval development and metamorphosis in Mytilus coruscus. Exposure to 4.7 and 39.2 μg/L PFOS and 1.2, 7.5, and 91.8 μg/L F53B significantly reduced larval metamorphosis compared to controls. PFOS and F53B exposure disrupted the normal degeneration of the larval velum and velum retractor muscles, essential for metamorphosis. Lower concentrations (1.2 and 7.5 μg/L) of F53B had a stronger inhibitory effect than 91.8 μg/L, suggesting F53B may act as an endocrine disruptor. Transcriptomic analysis revealed 801 differentially expressed genes in PFOS-exposed larvae and 2496 DEGs in F53B-exposed larvae, affecting pathways related to neural communication, cellular processes, and developmental signaling (e.g., Hedgehog, PI3K-AKT, Hippo, and MAPK). Real-time quantitative polymerase chain reaction confirmed the down-regulation of genes related to growth and development in both treatment groups, indicating suppressed growth and development. Our findings suggest that PFOS and F53B impacted larval metamorphosis and potentially altered the developmental trajectories of M. coruscus under environmental contamination scenarios. This study highlights the significant ecological implications of PFOS and F53B exposure on marine bivalve development, demonstrating their capacity to disrupt larval metamorphosis, thereby underscoring the potential risks these persistent pollutants pose to marine ecosystems and the early life stages of aquatic organisms.