A novel composite, polydopamine-modified Mo2C/MoO2 nanoparticles (HD-Mo2C/MoO2), as anode electrocatalyst for microbial fuel cells (MFCs), is synthesized via carbon thermal reduction and following in situ polydopamine modification. The physical and electrochemical characterizations show that Mo2C/MoO2 nanoparticles can be well dispersed through polydopamine modification and the resulting HD-Mo2C/MoO2 exhibits excellent electrocatalytic activity compared with unmodified Mo2C/MoO2. The MFC using HD-Mo2C/MoO2 as anode electrocatalyst achieves a maximum output power density of 1.64 ± 0.09 W m−2, which is 39% higher than that using Mo2C/MoO2 (1.18 ± 0.08 W m−2) as anode electrocatalyst. This excellent performance is attributed to modification of PDA, HD-Mo2C/MoO2 shows better hydrophilicity and electrocatalytic activity toward the direct oxidation of bacterial metabolites than unmodified Mo2C/MoO2.