This research the bait microalgae Chlorella sp. and Isochrysis zhangjiangensis were fed to Ruditapes philippinarum (clams) using two types of cultures, monoculture and co-culture, simulating the conditions, and presence, of common heavy metals Cu2+, Pb2+ and Cd2+ in cultured waters. The effects of microalgae growth, antioxidant activity, and changes in nutrient TN and TP were investigated. The metal contents of the culture solution, algal cells, and four tissues of Ruditapes philippinarum were analyzed. The results showed that the highest nutrient removal efficiency was achieved under the co-culture of three heavy metals, with the removal rates of TN and TP ranging from 47.26% to 51.36% and 78.28% to 87.72%, respectively. The higher tolerance of Chlorella sp. to heavy metals compared to Isochrysis zhangjiangensis was probably due to the higher glutathione and super oxide dimutase activities exhibited by Chlorella sp. cells, which increased by 28% and 40.64%, respectively. Isochrysis zhanjiangensis, Chlorella sp. and their co-culture group had the highest removal rate of Pb2+, which were 20.15%, 26.56% and 29.19%, respectively, followed by Cd2+ and Cu2+. The enrichment of the four tissues from the Ruditapes philippinarum organism for heavy metals, was in the order of visceral mass > gill > coat membrane > muscle. The biotransfer coefficients of the three metals in the microalgae-Ruditapes philippinarum food chain biomagnification ranged from 0.24 to 0.79, which indicated that there was no significant biomagnification of the metals in the transfer process of the food chain. The results of this study reveal the mechanism of heavy metal transport in the algae-shellfish system, which would provide a theoretical basis for improving the ecological environment, and can improve the quality of cultured shellfish products.