The removal rates of different carbon sources (acetic acid, fulvic acid) and total nitrogen in simulated biogas slurry was investigated in microbial electrolysis cell (MEC) under different voltage conditions, and the changes of microbial community structure were analyzed. With acetic acid as the carbon source, NO₃ ⁻-N was almost completely removed, and the chemical oxygen demand (COD) removal rate was stable at about 72%. With fulvic acid as the carbon source, the NO₃ ⁻-N and COD removal rates dropped to 40%～50% and 50%～60%, respectively. Comparatively, the removal efficiencies of COD and total nitrogen in MEC were more stable under the voltage of 0.2～0.4 V. Under the higher voltage of 0.8 V, the removal rate of NO₃ ⁻-N rose to 52% but the total nitrogen removal rate dropped to (32.4±3.7)%. High-throughput sequencing results showed that the applied voltage can effectively improve the ability of microbial flora to resist the shock of substrate loading, and it also increase the bacterial diversity and abundance in MEC. Among them, the abundance of autotrophic denitrifying bacteria Thanuera increased from 4.35% to 7.65%. In the MEC reactor with fulvic acid as the carbon source, a variety of bacteria that play a role in anaerobic nitrification were activated and enriched, such as Anaerolineae, which abundance was increased to 11.16%. The relative abundance of Anammox bacteria Planctomycetota was increased from 0.41% in the control group to 1.59%.