The potential distribution at the membrane-solution interface (Donnan potential) is critical for ion transport in the nanochannel. Herein, a charge-enhanced electrically responsive membrane with a tunable pore size is prepared to investigate the impact of the Donnan effect on ion transport in negative nanochannels of varying sizes. Both the Donnan effect and pore size changes influence ion transport within nanochannels, with an enhanced Donnan effect promoting cation transport while slowing anion permeation. The combined effect of the electrostatic interaction and steric sieving expands the membrane rejection adjustment range from 9.6% to 27.6%, as the applied voltage simultaneously decreases pore size and increases Donnan exclusion. The reduction in pore size enhances the ability of the per unit of Donnan potential to regulate ion transport, and electrostatic exclusion is more pronounced in smaller nanochannels. The same conclusion is confirmed in commercial nanofiltration membranes of varying sizes (NF270 and NF800), but as the nanochannel size decreases further (NF90), the effect of electrostatic interaction on ion transport becomes minimal. Since the nanochannels are too narrow to permit ion transport, size sieving becomes the dominant mechanism for selective separation. This work enhances our understanding of ion transport in nanochannels and supports the development of high-performance nanofiltration membranes.