Microbial fuel cells (MFCs) with different electrode configurations were constructed to study the mechanism of influence of multiple current paths on their electrical performance and the removal of heavy metals in soil. Three types of MFCs were constructed, namely, double anode–single cathode (DASC), single anode–dual cathode (SADC), and single anode–single cathode (SASC). The total electricity generation of the three kinds of MFC was similar: 143.44 × 10–3 mW, 114.90 × 10–3 mW, and 132.50 × 10–3 mW, respectively. However, the maximum voltage and cathode current density produced by a single current path differed significantly. The corresponding values were 0.27, 0.23, and 0.42 V and 0.130, 0.122, and 0.096 A/m 2, respectively. The SASC had the best electricity generation performance. Based on a limited reduction rate of oxygen at the cathode, the accumulation of cathode electrons was facilitated by the construction of multiple current paths in the MFC, which significantly increased the cathode electron transfer resistance and limited the electricity generation performance of the MFC. However, at the same time, the construction of multiple current paths promoted output of more electrons in the anode, reducing the retention of anode electrons and anode electron transfer resistance. The heavy metal removal efficiencies of SASC, DASC, and SADC were 2.68, 2.18, and 1.70 times that of the open circuit group, respectively. The migration of heavy metals in the soil depended mainly on the internal electric field intensity of the MFC rather than the total electricity generation. As the internal electric field intensity increased, the removal efficiency of heavy metals in the MFC increased.