 Enhancing anode performance is a critical step to improving the power output and energy storage of microbial fuel cells (MFCs). In this study, MFCs containing pseudocapacitive anode materials, such as polypyrrole-carboxymethyl cellulose (PPy-CMC) composite films, were used to coat the nitrogen-doped carbon nanotube (N-CNT)/sponge (S) for use in MFCs. The capacitive anode could function as a bioanode, store electrons generated from the microbial oxidation of a substrate, and release the accumulated charge as needed. Scanning electron microscopy results indicated that the composite anode had a three-dimensional macroporous structure with a large specific surface area, providing more sites for microbial attachment and growth. Experimental results showed that MFCs equipped with PPy-CMC/N-CNT/S capacitive bioanodes had a maximum power density of 4.88 W m−3, which was 1.34 and 1.71 times as much as those of PPy/N-CNT/S and N-CNT/S bioanodes (3.65 and 2.85 W m−3), respectively. Moreover, the charge–discharge time of 60–90 min, the total charge Qm of the MFC equipped with the PPy-CMC/N-CNT/S anode was the largest (5154.08 mC cm−2)—5.7 times higher than that of the N-CNT/S anode. The excellent performance of the MFC equipped with the PPy-CMC/N-CNT/S anode was attributable to the composite materials, which exhibited a large-pore structure, good biocompatibility, large capacitance, and high specific surface area. Therefore, this synthesized composite exhibited potential as a capacitive and biocompatible anode material in MFCs.