Water contamination resulting from the presence of the various coexistent pollutants is an urgent environmental challenge, and effective treatment is demanded to remove the toxic substances. The removal of pollutants by adsorption, as an effective, efficient and economic strategy, has been widely used in water treatment. In this work, PEI@MCM-41 was prepared by infiltrating polyethyleneimine (PEI) into the pores of mesoporous MCM-41, and applied for the removal of heavy metal ions. The adsorption kinetics of Cu2+, Ni2+ and Cd2+ by PEI@MCM-41 were supposed to be pseudo-second-ordered, and the adsorption capacities were as high as 39.30, 33.67 and 21.10 mg·g−1, respectively. The influence of temperature, pH, coexistent salt and heavy metal ions concentration on the adsorption performance was studied. Owing to the nanoconfinement effect and hydrogen bond, PEI remained stable during the adsorption and desorption process, and the adsorption capacity for Cu2+ maintained 84.15 % even after four consecutive adsorption–desorption cycles. This work demonstrates that the potential practical applicability of PEI@MCM-41 as promising adsorbent in the removal of heavy metal ions.