Azo dye pollution has become a worldwide issue, and the current treatment methods can hardly meet the expected emission standards. Microbial electrochemical systems (MESs) show promising applications for decolorization, but their performance critically depends on the microorganisms. Electrode modification is an interesting method of improving decolorization performance. However, the mechanisms of how the modification can affect microbial communities and the decolorization process remain unclear. Here, a modified anode with polyaniline (PANI) and graphene was fabricated via electro-deposition. Consequently, the highest decolorization efficiency was obtained. The Congo red (CR) decolorization rate of the MESs with the PANI/graphene-modified electrode (PG) reached 90% at 54 h. By contrast, the CR decolorization rates of the MESs with the PANI-modified electrode (P) and those of the MESs with the unmodified electrode (C) only reached 68% and 79%, respectively. Results of the microbial community analysis showed abundant Methanobrevibacter arboriphilus in PG (11%), which was 5.5 times that in C (2%) at 18 h. This phenomenon may be related to the rapid decolorization. The upregulated metabolism pathways, including arginine and proline metabolism, purine metabolism, arginine biosynthesis, and riboflavin metabolism, provided more electron shuttles and redox mediators that facilitated the extracellular electron transfer. Therefore, the PG-modified electrode facilitated the decolorization by altering certain metabolic pathways. This study can help to improve the guideline on the potential application of MESs for wastewater treatment.