The main challenge in separating molybdenum(VI) and vanadium(V) which have similar properties results in great difficulties in the green recycling of hazardous spent catalysts. Here, selective facilitating transport and stripping are integrated into the polymer inclusion membrane electrodialysis process (PIMED) to separate Mo(VI) and V(V) to overcome the complicated co-extraction and stepwise-stripping in conventional solvent extraction. The influences of various parameters, the selective transport mechanism, and respective activation parameters were systematically investigated. Results revealed that the affinity of the Aliquat 36 as the carrier and PVDF-HFP as the base polymer of PIM towards Mo(VI) is stronger than that of V(V), while the strong interaction between Mo(VI) and carrier caused low migration through the membrane. By the combination of adjusting and controlling the electric density and strip acidity, the interaction was destroyed and the transport was facilitated. After optimization, stripping efficiencies of Mo(VI) and V (V) increased from 44.4% to 93.1% and reduced from 31.9% to 1.8%, respectively, while their separation coefficient increased 16.3 times to 333.4. The activation energy, enthalpy and entropy for the transport of Mo(VI) were determined to be 4.846 kJ mol−1, 6.745 kJ mol−1 and − 310.838 J mol−1 K−1, respectively. The present work demonstrates that the separation of similar metal ions could be improved by fine tuning the affinity and interaction between metal ions and the PIM, thus providing new insights into the recycling of similar metal ions from secondary resources.