In order to protect the ecological environment on which human beings depend, it is of great practical significance to prevent and control the heavy metal pollution in surface water. Cr(VI) in anionic form and Cd(II) in cationic form were selected to conduct the heavy metal purification experiments. Cr(VI) and Cd(II) removal by constructed rapid infiltration systems (CRIS) contain Zn-CO3-LDHs (ZnAl-CO3-LDHs and ZnFe-CO3-LDHs) coated maifanite substrates were compared. After ZnAl-CO3-LDHs coated, the Cr(VI) and Cd(II) removal amount increased by 87.53 % and 19.00 %, respectively. It could be inferred from XRD, FTIR, and Zeta potential results that the Cr(VI) physicochemical removal mechanism of maifanite changed to anion exchange, chemical bonding and electrostatic adsorption from electrostatic adsorption and chemical bonding after Zn-CO3-LDHs coated. By contrast, isomorphous replacement, electrostatic adsorption and chemical bonding of Cd(II) induced by Zn-CO3-LDHs replaced the electrostatic adsorption by natural maifanite. Additionally, the effective Cr(VI)/Cd(II) accumulation on Zn-CO3-LDHs modified maifanite reduced the microbial quantity, but increased EPS secretion and changed the community structure, which achieved the microbial Cr(VI)/Cd(II) removal through extracellular complexation and intracellular accumulation. This research result may provide essential reference for exploring the feasibility of heavy metal removal of CRIS with LDHs modified substrate.