The addition of physical field enhancement measures to improve the purification effect of vertical flow artificial wetlands has gradually become popular. In this study, a vertical flow artificial wetland system reinforced by electric and magnetic fields was constructed. These fields were first optimized using finite element 3D simulation software to obtain the optimal electric and magnetic field parameters. Then, the pollutant removal effects and changes in microbial community structure were comparatively analyzed. The optimal electromagnetic field parameters (applied voltage of 15 V and applied magnetic field of 20 mT) resulted in significantly enhanced removal rates of chemical oxygen demand (COD), nitrate nitrogen (NH4+-N), total phosphorus (TP), and orthophosphorus (PO43−-P) in wastewater, with rates of 74.47%, 45.44%, 89.85%, and 90.04%, respectively. These rates were notably higher than those observed in the vertical flow artificial wetland system. The microbial community structure analysis revealed that the vertical flow constructed wetland with enhanced electric and magnetic fields exhibited (EM-VFCW) a more diverse and complex microbial community structure. Notably, the abundance of bacteria capable of removing NH4+-N and COD, including Aspergillus, Fusarium, and Actinobacteria, was significantly elevated.