As the regulator of constructed wetlands (CWs), biochar is often used to enhance pollutant removal and reduce greenhouse gas emission. Biochar is proved to have certain effects on microbial populations, but its effect on the aggregation of microbial flocs and the formation of biofilms in the CWs has not been thoroughly investigated. Therefore, the above topics were studied in this paper by adding a certain proportion of biochar in aerated subsurface flow constructed wetlands. The results indicated that after adding biochar in the CWs, pollutant removal was enhanced and the removal rate of NH4+-N was increased from 80.76% to 99.43%. The proportion of hydrophobic components in extracellular polymeric substances (EPS) was reduced by adding biochar from 0.0044 to 0.0038, and the affinity of EPS on CH3-SAM was reduced from 5.736 L/g to 2.496 L/g. The weakened hydrophobic and the reduced affinity of EPS caused the initial attachment of microorganisms to be inhibited. The relative abundance of Chloroflexi was decreased after adding biochar, reducing the dense structural skeleton of biofilm aggregates. Correspondingly, the abundance of Bacteroidetes was increased, promoting EPS degradation. Biochar addition helped to increase the proportion of catalytic active proteins in extracellular proteins and decrease the proportion of binding active proteins, hindering the combination of extracellular proteins and macromolecules to form microbial aggregates. Additionally, the proportions of three extracellular protein structures promoting microbial aggregation, including aggregated chain, beta-sheet, and 3-turn helix, were decreased to 23.83%, 38.37% and 7.76%, respectively, while the proportions of random coil and antiparallel beta-sheet that inhibited microbial aggregation were increased to 14.11% and 8.11%, respectively. An interesting conclusion from the experimental results is that biochar not only can enhance pollutants removal, but also has the potential of alleviating biological clogging in CWs, which is of great significance to realize the sustainable operation and improve the life cycle of CWs.