Ion transport in nanoconfinement differs from that in bulk and has been extensively researched across scientific and engineering disciplines 1–4 . For many energy and water applications of nanoporous materials, concentration-driven ion diffusion is simultaneously subjected to a local electric field arising from surface charge or an externally applied potential. Due to the uniquely crowded intermolecular forces under severe nanoconfinement (<2 nm), the transport behaviours of ions can be influenced by the interfacial electrical double layer (EDL) induced by a surface potential, with complex implications, engendering unusual ion dynamics 5–7 . However, it remains an experimental challenge to investigate how such a surface potential and its coupling with nanoconfinement manipulate ion diffusion. Here, we exploit the tunable nanoconfinement in layered graphene-based nanoporous membranes to show that sub-2 nm confined ion diffusion can be strongly modulated by the surface potential-induced EDL. Depending on the potential sign, the combination and concentration of ion pairs, diffusion rates can be reversibly modulated and anomalously enhanced by 4~7 times within 0.5 volts, across a salt concentration gradient up to seawater salinity. Modelling suggests that this anomalously enhanced diffusion is related to the strong ion–ion correlations under severe nanoconfinement, and cannot be explained by conventional theoretical predictions.