BACKGROUND: The nutritional compositions of abalones (Haliotis discus hannai) vary with geographical origins and environmental factors. Traceability is an important part of food safety, and the heavy metals in the aquatic environment pose a threat to living organisms. Therefore, we present a comparative analysis of the nutrient and heavy metal content in abalones from three different sea areas in China: the Bohai Sea, East China Sea, and South China Sea. This study uniquely addresses the correlation between nutrient composition and heavy metal accumulation. By employing weighted gene co-expression network analysis, we reveal the biological implications of heavy metal exposure, specifically focusing on chromium, copper (Cu), manganese, zinc, arsenic (As), cadmium, and lead. RESULTS: Betaine, glycine, and glycogen appeared in three comparisons. The abalone in the East China Sea had the highest content of betaine, and the abalone in the South China Sea had the highest contents of glycine and glycogen. Among the measured metals, the heavy metals accumulated in the viscera were significantly higher than that in the muscle, except Cu, and As showed a high target hazard quotient and carcinogenic risk. CONCLUSION: Betaine, glycine, and glycogen might be important indicators for origin traceability of abalone. Abalones from the South China Sea provide higher nutritional value. Cu had different accumulation patterns and As showed high health risks, and heavy metals brought oxidative stress to abalone. Our findings not only contribute to the understanding of abalone safety and quality but also provide a novel approach to assessing impact of heavy metals on marine food sources. © 2025 Society of Chemical Industry.