The nanometer effect in the process of arsenic ions removal on α-MnO2 nano-surface is studied by first-principles method through microfacet models. Several parameters, such as adhesion energy, electrostatic potential, Mulliken population were calculated to illuminate the internal mechanism. The results show that the adsorption energies of As(OH)3 molecules on MnO2[(100×110)] nanostructure are smaller than that on bulk surface with the same concentration, which means the nanometer effect is beneficial to enhance the adsorption ability of MnO2 nano-surface. In aqueous solution, there exist two possible removal ways of As ions. One is the direct reaction of As(OH)3→As(OH)6-, which occurs both in bulk surface and nano-surface. However to nanomaterials, there exists another removal way of As(OH)3→As(OH)4→As(OH)6- through an intermediate As(OH)4 molecule produced by nanometer effect. Furthermore the smaller electrostatic potential of As ions on [(100×110)] nano-surface is beneficial to enhance the removal capability of As ions. Then the reason why MnO2 nanomaterials have better catalytic activity than the bulk materials is originated from its much less adhesion energy, much more removal ways and much smaller electrostatic potential. So this research provides a detailed understanding on the removal capability of toxic ions influenced by nanometer effect.