Persistent organic pollutants (POPs) are easily accumulated in organisms due to its high lipophilicity. Bivalves are still one of the marine invertebrates with high species diversity despite experiencing with environmental pollution. However, studies investigating the adaptation mechanisms of bivalves towards POPs have been lacking. In this study, we chose benzo[a]pyrene (B[a]P), a typical POPs, to investigate the accumulation and excretion mechanism of clam Ruditapes philippinarum towards B[a]P. Laser confocal microscopy images of ovaries and testes confirmed significant colocalization between lipid droplets and B[a]P. However, B[a]P in the testes might mainly excrete with the excretory fluid. Furthermore, lipidomics results indicated that the upregulated TGs were TGs with 48-58 total carbon atoms and 6-12 double bonds in acyl side chains in ovaries, while the upregulated TGs mainly distributed in 48-58 total carbon atoms and 4-14 double bonds in acyl side chains in testes. In ovaries, gene expression of lipid metabolism and phospholipid metabolism basically presented an upward trend at Pro and Mat stages, while entirely performed a downregulation trend at Gro stage. Testes had the opposite regulation with that. Additionally, B[a]P prompted the excretion ability of female clams, but exhibited a complex effect in the male. This study provides a scientific basis for bivalve toxicology and healthy aquaculture, which is of great significance for marine ecological environment protection and aquatic product safety of China. Environmental ImplicationBivalves are an ancient class of animals that appeared 500 million years ago, and are still one of the marine invertebrates with high species diversity despite experiencing with global climate change and environmental pollution. Thus, explore the adaptation mechanism of bivalves under contaminant stress can generate responses for biodiversity conservation. In this study, we investigate the accumulation and excretion mechanism of clam Ruditapes philipinarum towards B[a]P. The results will provide a scientific basis for the protection of germplasm resources and healthy aquaculture, which is of great significance for marine ecological environment protection and aquatic product safety of China.