The microbial electrochemical system (MES) holds promise for in synchronously wastewater treatment and resource utilization, yet it is hampered by suboptimal electron transfer efficiency between the electrode and exoelectrogen. Generating highly active biofilms and facilitating efficient electron exchange at the anode-bacteria interface are critical for MES enhancement. Customization of electrode components and structure can be achieved through endogenous modification of the carbonizing precursor. Herein, we introduced oxygen-containing groups and heteroatoms into the carbon skeleton by doping with humic acid during the fabrication of phenolic-based carbon electrodes. This process was further refined by combining endogenous humic acid doping with controlled pore generation techniques using an anionic active agent and sacrificial templates, establishing a dual-channel optimization strategy for component and structural regulation. Consequently, the resulting sodium humic acid-modified porous electrodes (SHEs) exhibited superior wettability (48 ± 1.5°) and enhanced redox activity owing to their rich oxygenic functional groups. The hierarchical porous architecture and roughened surface texture of the SHEs contributed to their notable capacitance (1280 mF) and biocompatibility. Specifically, the SHEPS samples achieved the highest energy density of 4200 ± 48 mW m−2 and fostered a biofilm with Geobacter content of 78%. The synergistic interaction between exoelectrogens and non-exoelectrogens bolstered the electrochemical performance and stability of the biofilm. This study introduces a novel approach for the synchronous regulation of endogenous components and structure, guiding the design of high-performance, free-standing 3D electrodes for MES applications. These electrodes promote the development of highly electrochemically active biofilms and efficient energy capture, propelling MES towards practical implementation.