Optimizing the structure of electrode materials is one of the most effective strategies for designing high‐power microbial fuel cells (MFCs). However, electrode materials currently suffer from a series of shortcomings that limit the output of MFCs, such as high intrinsic resistance, poor electrolyte wettability, and low microbial load capacity. Here, a three‐dimensional (3D) nitrogen‐doped multiwalled carbon nanotube/graphene (N‐MWCNT/GA) composite aerogel is synthesized as the anode for MFCs. Comparing nitrogen‐doped GA, MWCNT/GA, and N‐MWCNT/GA, the macroporous hydrophilic N‐MWCNT/GA electrode with an average pore size of 4.24 µm enables high‐density loading of the microbes and facilitates extracellular electron transfer with low intrinsic resistance. Consequently, the hydrophilic surface of N‐MWCNT can generate high charge mobility, enabling a high‐power output performance of the MFC. In consequence, the MFC system based on N‐MWCNT/GA anode exhibits a peak power density and output voltage of 2977.8 mW m−2 and 0.654 V, which are 1.83 times and 16.3% higher than those obtained with MWCNT/GA, respectively. These results demonstrate that 3D N‐MWCNT/GA anodes can be developed for high‐power MFCs in different environments by optimizing their chemical and microstructures.