Functionalization of graphene enables precise control over interlayer spacing during film formation, thereby enhancing the separation efficiency of radioactive ions in graphene membranes. However, the systematic impact of interlayer spacing of graphene membranes on radioactive-ion separation remains unexplored. This study aims to elucidate how interlayer spacing in functionalized graphene membranes affects the separation of radioactive ions. Utilizing polyamidoxime (PAO) to modify graphene oxide, we controlled the interlayer spacing of graphene membranes. Experimental results indicate that tuning interlayer spacing enables control of the permeation flux of radioactive ions (UO22+ 1.01 × 10−5–8.32 × 10−5 mol/m2·h, and K+ remains stable at 3.60 × 10−4 mol/m2·h), and the K+/UO22+ separation factors up to 36.2 at an interlayer spacing of 8.8 Å. Using density functional theory and molecular dynamics simulations, we discovered that the effective separation is mainly determined via interlayer spacing and the quantity of introduced functional groups, explaining the anomalous high permeation flux of target ions at low interlayer spacing (4.3 Å). This study deepens our comprehension of interlayer spacing within nanoconfined spaces for ion separation and recovery via graphene membranes, offering valuable insights for the design and synthesis of high-performance nanomembrane materials.