Micro-polluted water, which is widespread in rural areas, poses a serious health risk. To address this issue, we propose a three-dimensional biofilm electrode reactor with triple-layer particle electrodes (TL-BERs) for the decentralized and small-scale treatment of micro-polluted water. The first and second layers of the electrode, granular activated carbon (GAC) and biological ceramsite (BC), respectively, are responsible for electric field oxidation and microbial degradation, respectively, while the third, quartz sand (QS), is responsible for further improving turbidity and pollutant removal. Our tests indicated that the TL-BER-treated effluent met the drinking water quality standards of China. At 10 V, the average turbidity, CODMn, NH4+-N, and UV254 removal rates of the TL-BERs system were 97.66%, 61.11%, 91.67%, and 72.94%, respectively. Furthermore, the intensities of the main fluorescence peaks, A, B, C, and D, of the raw water sample, decreased by 36.67%, 66.22%, 67.08%, and 69.76%, respectively, after treatment, indicating that tryptophan-like proteins, fulvic acid, and humic acid were also effectively removed. High-throughput sequencing analysis showed the enrichment of microorganisms, such as Proteobacteria, Bacteroidota, and Actinobacteriota, which play important roles in the removal of various pollutants. Therefore, the application of this strategy will enable the practical treatment of micro-polluted water.