Selection of inoculum sources is a key factor in constructing microbial fuel cells (MFCs), and the property of inoculum sources is greatly affected by the degree of environmental pollution. However, limited attention has been paid to how these differences affect the response of MFC biosensors. Here the effects of inoculum sources with varying pollution levels on the performances of constructed MFCs were evaluated, and the microbial communities were analyzed before and after inoculation. The results showed significant differences in the detection of biochemical oxygen demand (BOD) and toxicity (Cu2+) among the five groups of MFC biosensors. Combined with the data of the microbial community, the results indicated that the increase rate of the initial start-up voltage is related to the abundance of original electroactive bacteria (EAB) in the inoculum source. The higher the abundance of EAB, the faster increase rate in the initial start-up voltage and the shorter start-up time. The difference in the detection range of the BOD should be related to the ability of the microbial communities to withstand the organic shock loads. The microbial community's tolerance to Cu2+ was affected by the original water quality of the inoculum source. The high metal ion content leads to low sensitivity of MFC biosensor to Cu2+ ion. Enterobacteriaceae were abundant in all the five groups of MFCs, indicating that the dominant bacteria can be enriched in MFC anode biofilms with the inoculum sources of different pollution levels. The microbial community compositions of the anode biofilms were affected by the inoculum sources of different pollution levels, which in turn resulted in the differences in MFCs performances.