The low power generation efficiency of microbial fuel cells (MFCs) is always a barrier to further development. An attempt to enhance the start-up and electricity generation of MFCs was investigated by adding different doses of zero-valent iron into anaerobic anode chambers in this study. The results showed that the voltage (289.6 mV) of A2 with 0.5 g of zero-valent iron added was higher than the reference reactor (197.1 mV) without dosing zero-valent iron (A4). The maximum power density of 27.3 mW/m2 was obtained in A2. CV analysis demonstrated that A2 possessed a higher oxidation–reduction potential, hence showing a stronger oxidizing property. Meanwhile, electrochemical impedance analysis (EIS) also manifested that values of RCT of carbon felts with zero-valent iron supplemented (0.01–0.03 Ω) were generally lower. What is more, SEM images further proved and illustrated that A2 had compact and dense meshes with a hierarchical structure rather than a relatively looser biofilm in the other reactors. High-throughput sequencing analysis also indicated that zero-valent iron increased the abundance of some functional microbial communities, such as Acinetobacter, Ignavibacteriales, Shewanella, etc.