The electro-Fenton oxidation process for the degradation of organic pollutants in recalcitrant wastewater has garnered significant attention and research efforts in the field of advanced water treatment. This is primarily due to its highly effective degradation capabilities and the advantages it offers, including the avoidance of unsafe transportation and storage of hydrogen peroxide (H2O2). However, challenges such as relatively high energy consumption, complex operational requirements, and limited operational stability continue to pose significant economic constraints on the widespread application of electro-Fenton technology in water purification. In this study, we employed a secondary hydrothermal method to construct a multi-layered CNT/MoS2/Fe3O4 composite heterostructure in situ. Leveraging the synergistic effects of the introduced variable valence elements, Fe and Mo, and the interconnected multi-layered membrane structure, the CNT/MoS2/Fe3O4 electro-Fenton membrane holds promise in a permeable filtration system. Under the conditions of a current density of 1.50 mA/cm² and an electrolyte concentration of 0.50 mol/L, the CNT/MoS2/Fe3O4 composite membrane exhibited a degradation efficiency of over 90.00 % for 100.00 mg/L RhB within 10 minutes, and the degradation rate approached nearly 99.00 % at 60 minutes. Furthermore, the degradation efficiency for various recalcitrant organic dye wastewaters, including phenol, methyl orange, and methylene blue, could be maintained at levels ranging from 80.00 % to 97.00 %. Particularly, under optimized operating conditions, the specific energy consumption (EC) for the CNT/MoS2/Fe3O4 membrane process was measured at 0.60±0.01 kWh/m³, showcasing exceptionally low energy consumption characteristics. In conclusion, it is expected to contribute to the reduction of the overall consumption of heterogeneous electro-Fenton oxidation systems and enhance their operational efficiency. This innovative approach represents a significant advancement in the field, offering the potential to address the economic limitations associated with electro-Fenton technology in water quality purification.