Abstract: To investigate the removal of heavy metal ions from shellfish by-products by modified mesoporous materials, the silicon-based mesoporous material SBA-15 grafted with different groups (2-mercaptothiazoline 2-mercaptobenzothiazole, and ammonium pyrrolidine dithiocarbamate) were prepared by post-grafted and characterized by mesopore pore size distribution, the standard solutions of four heavy metal ion lead, chromium, cadmium, and copper were used to investigate the adsorption capacity of the mesoporous materials. The optimal pH values, adsorption equilibrium time and adsorption quantities of different concentration of metal ions were studied. And the APDC-SBA-15 material was adopted to remove heavy metals in by-products of shellfish products. The removal rates of heavy metal ions and the loss rates of other nutrients were examined. The results showed that, three kinds of mesoporous materials (MT-SBA-15, MBT-SBA-15, APDC-SBA-15) were prepared successfully with optimal pore parameters. The optimal pH was 6.0, the adsorption equilibrium time was 30 min, and when the concentration of four standard metals was 1200 mg/L, the adsorption was largest for the three mesoporous materials. The adsorption capacity of APDC-SBA-15 for heavy metals was the largest among the three mesoporous materials, the maximum adsorption capacities for Pb, Cr, Cd, and Cu were 223.6, 240.0, 259.8 and 259.0 mg/g. The APDC-SBA-15 mesoporous material was adopted to remove heavy metals in cooking liquor of Ruditapes philippinarum, the removal rate of lead was 100.00%, and the loss rate of polysaccharide was 7.32%. The removal rates of lead was 84.50%, and the loss rate of polysaccharide was 2.57% when the APDC-SBA-15 mesoporous material was adopted in polysaccharide of Ruditapes philippinarum. When the APDC-SBA-15 mesoporous material was adopted in peptides of oysters, the removal rates of lead and chromium were 62.20% and 100.00%, respectively, and the loss rate of proteins was 14.62%. The APDC-SBA-15 mesoporous material could efficiently remove heavy metals and the loss rates of proteins and polysaccharides were low.