The adsorption of heavy metals on allophane has been extensively studied due to the properties of allophane special. However, the difference in adsorption behaviors and mechanisms of a metal cation and metal anion on allophane remains uncertain. The present study aimed to investigate the removal of Pb(II) and Cr(VI) onto synthetic allophane under variable pH, initial Pb(II) and Cr(VI) concentrations, and contact time. The results showed that the maximum adsorption capacity of allophane for Pb(II) and Cr(VI) was 88 and 8 mg/g, respectively. Equilibrium adsorption for Pb(II) was achieved in 12 h for Cr(VI). The response to changes in pH indicated the occurrence of electrostatic adsorption occurred during Cr(VI) absorption. XPS analysis suggested that reactions between predominant surface functional groups of allophane (Al-O- and Si-O-) and Pb(II) occurred through the formation of P-O bonds. The uptake mechanism of Pb(II) was based on a chemical reaction rather than a physical adsorption process. Synthetic allophane holds great potential to effectively remove aqueous metal ions for special wastewater treatment applications.