Microbial fuel cells (MFCs) as green and sustainable technology for power generation still face various obstacles such as the lower power generation. In this work, a kind of phosphate-derived composites using ZIF-67 (Co–Ni-ZIF/P) as framework was prepared and employed it as anode in MFC. Results demonstrated that the Co–Ni-ZIF/P anode could reduce the electron transfer resistance and simultaneously improve the bioelectrocatalytic activity of the anode and microbial colonization. The maximum energy output of MFC with Co–Ni-ZIF/P anode reached 4.511 W m−3, which was 2.18 times larger than that of MFC with Co–Ni-ZIF anode (2.07 W m−3). Microbial community structure analysis proved that more electrochemically active microbial species were attracted on the proposed anodes, and their synergistic effect could facilitate the extracellular electron transfer (EET) process. In particular, Geobacter was the most typical exogenous electron-producing enriched on the Co–Ni-ZIF/P anode with a relative abundance of up to 60.83%. The present work offers a promising prospect for the application of bio-functional ZIF for the high-performance anode construction of MFCs.