Ultraviolet (UV) filters represent a new class of micropollutants in water. To effectively remove these substances and minimize fouling during ultrafiltration, an electro-ultrafiltration process was used to separate benzophenone-3 (BP-3) from water by applying an electric field across the membrane. The effects of the electric field on the filtration performance, including resistance and retention, modification of polyvinylidene fluoride (PVDF) membrane and possible intermediates produced during electro-ultrafiltration, were studied thoroughly. The results clearly indicate that the combination of the electric field with ultrafiltration could increase BP-3 rejection and reduce filtration resistance. The membrane had a rougher surface and the pore size increased due to the modifications of PVDF membrane induced by the electric field. The decrease in contact angle demonstrated the improvement of hydrophilicity in the PVDF membrane surface after the electrofiltration treatment. The mechanism of BP-3 degradation in the electrofiltration was examined theoretically by calculating the frontier electron densities of the BP-3 molecule. The C3 atom in the BP-3 structure was demonstrated to be the most reactive site, which was consistent with the intermediate results identified by gas chromatography-mass spectrometry (GC-MS) analysis.