Herein, a novel triple-layered heterojunction catalytic cathode membrane (PVDF/rGO/TFe/MnO2, TMOHccm) was reported and applied in seawater electro membrane reactor assisted electrolytic cell system (SEMR-EC), achieving increased properties for cyanide wastewater treatment. Hydrophilic TMOHccm exhibits higher electrochemical activity (qT* 1.11 C cm−2, qo* 0.03 C cm−2), indicating excellent electron transfer efficiency. Further analysis shows a one-electron redox cycle of exposed transition metal oxides (TMOs) on rGO support mediated oxygen reduction reaction (ORR) process, and calculated results of density functional theory (DFT) demonstrates positive Bader charge (72 |e|) of synthesized catalyst. The developed SEMR-EC was implemented in intermittent-stream operation for treating cyanide wastewater, the system achieved optimized decyanation and carbon removal performance (CN− 100%, TOC 88.49%). Hyperoxidation active species produced SEMR-EC including hydroxyl, sulfate, and reactive chlorine species (RCS) was confirmed. The proposed mechanistic explanation indicated multiple removal pathways relevant to cyanide, organic matter, and iron were elucidated, and the engineering applications prospects were highlighted by cost (5.61 $) and benefit (Ce 399.26 mW m−2 $−1, EFe 248.11 g kWh−1) analysis of the system.