The invention relates to a microbial fuel cell system with a chemically modified biological cathode. The system comprises an anode chamber, a cathode chamber, as well as a proton exchange membrane between the anode chamber and the cathode chamber; the anode chamber is composed of an anolyte and an anode; the cathode chamber is composed of a catholyte and a cathode; the system further comprises a conducting wire connected with the anode and the cathode, and a circuit resistor on the conducting wire; a chemical modification layer is loaded on the surface of the cathode; an aerobiont is vaccinated onto the chemical modification layer. Compared with the prior art, the microbial fuel cell system provided by the invention not only can provide better cathode catalytic performance and improve cathode potential, but also can provide an easy-for-apposition growth environment for aerobic microorganism vaccination, and is more favorable for the starting of an aerobic biocathode. The overall systemis simple and compact in structure, low in energy consumption during an operation process, achieves functions of synchronously absorbing and removing ammonia nitrogen by the cathode, and degrading pollutants by the anode, and integrally generating electricity, and has a very good development and application prospect.