The current efficiency (CE) of electrogeneration of H2O2 closely determines the cost of the electro-Fenton process and is influenced by two aspects: intrinsic activity of catalysts and application parameters. To understand how the two aspects interplay, in this study, oxidized carbon nanotubes are screened as catalysts and evaluated by comparing CE of H2O2 generation on a rotating ring-disk electrode (CERRDE) and CE on a gas diffusion electrode (CEGDE). The results show that CEGDE is evidently larger than CERRDE, the reason for which is ascribed to sufficient oxygen supply for the GDE, indicating that oxygen supply is more crucial than the intrinsic activity of catalyst. Using optimized parameters for electro-Fenton to treat simulated rhodamine B wastewater, it is shown that the removal efficiency of chemical oxygen demand (COD) is only 57% when rhodamine B is degraded by 99% and completely removing COD would cause much higher energy consumption. Therefore, electro-Fenton is only employed to pretreating refractory wastewater for enhancing the biodegradability. Tests with three types of wastewater confirm the general applicability of enhancing the biodegradability using short-time electro-Fenton treatment.