Abstract: In many parts of rural China, the scattered layout of villages presents complex challenges for wastewater treatment. Unlike urban environments, where centralized systems dominate, rural areas often face fragmented sewage sources, limited treatment capacity, and inadequate infrastructure. These practical constraints, combined with regional disparities in water quality, quantity, and economic capacity, make it difficult to apply a unified treatment model. As such, traditional urban wastewater solutions, particularly the activated sludge process, frequently fall short in rural contexts-leading to inefficiencies and unstable effluent outcomes. The "one-size-fits-all" approach of urban wastewater treatment technologies is unsuitable for rural regions, which require more targeted and flexible solutions to address location-specific conditions and constraints. To improve the functional performance of rural wastewater treatment, the conventional biofilter was modified by integrating a rotating biological contactor (RBC) with electromagnetic field (EMF) enhancement. This integrated approach aimed to bolster the system's tolerance to shock loading, improve pollutant adsorption, and foster a more active and stable microbial community by regulating growth conditions and stimulating metabolic activity. The resulting system-referred to as the electromagnetic field-enhanced rotating biological contact biofilter (EM-BF system)-was applied to treat domestic wastewater under varying operational conditions. A comprehensive evaluation of the EM-BF system was conducted, focusing on its treatment stability, pollutant removal efficiency, and microbial performance. High-throughput sequencing was employed to investigate shifts in microbial community structure and to elucidate the influence of EMF integration on microbial activity and ecological dynamics. Experimental results demonstrate that the EM-BF system achieved significantly higher removal rates of ammonium nitrogen (NH₄⁺-N) and total phosphorus (TP) (P < 0.05), along with enhanced resistance to load shocks. Effluent quality consistently met the Class 1A standards specified in Discharge Standard of Pollutants for Municipal Wastewater Treatment Plant (GB 18918-2002), with optimal performance observed at a hydraulic retention time (HRT) of 12 h. Under EMF stimulation, the system promoted the enrichment of nitrogen-cycling genera-including Lentimicrobium, Gemmatimonas, Nitrospira, Nitrosomonas, Denitratisoma, Hydrogenophaga, and Silanimonas-which contributed to improved nitrogen removal. Compared to the conventional biofilter, the EM-BF system maintained greater operational stability, with both pollutant removal and microbial composition less sensitive to pH fluctuations. These findings underscore the potential of EM-BF system for decentralized wastewater management, offering both practical efficacy and microbiological insight tailored to rural applications.