To understand the interaction mechanisms between heavy metals and functional groups modified nanomaterials, the l-cysteine (Cys) intercalated MgAl-layered double hydroxide (MgAl-Cys-LDH) was designed by a facile co-precipitation method and used to remove Cu(II), Pb(II) and Cd(II) in water solutions. The XRD, FTIR, SEM, TEM, EDS and XPS characterization analyses proved the carboxyl, thio and amido groups were successfully introduced into MgAl-LDH. The possible mechanisms were analyzed by the XPS and XRD spectra and involved the precipitation of metal hydroxides or sulfides, surface complexation with abundant surface groups, and the isomorphic substitution of Mg(II). The adsorption kinetics and isotherms data of Cu(II), Pb(II) and Cd(II) on MgAl-Cys-LDH were well described by the pseudo-second-order kinetic equation and the Langmuir model. The influence factors such as initial solution pH of heavy metals, dosage of MgAl-Cys-LDH, adsorption time and various types of water were investigated, and the results suggested that MgAl-Cys-LDH had potential applications in real wastewater treatment containing heavy metals.