Novel ultrafiltration membranes with both superior antibacterial and self-cleaning properties were fabricated. By using a non-solvent induced phase separation method (NIPS), N-halamine epoxide and siloxane were grafted onto the multi-walled carbon nanotubes (N-Si-MWNTs) to fabricate polyvinylidene fluoride (PVDF) hybrid membranes. The membrane morphology was observed under a field emission scanning electron microscopy. The results demonstrated that the PVDF hybrid membranes had an asymmetrical structure, and their hydraulic permeability was evidently enhanced with the addition of modified MWNTs. When compared with the primitive PVDF membrane, the hybrid membranes presented improved surface hydrophilicity. After three ultrafiltration–regeneration cycles with bovine serum albumin as model biofoulant and pure water as detergent, the PVDF hybrid membranes exhibited a high flux recovery ratio (FRR). Furthermore, when compared with other membranes, the membrane containing N-Si-MWNTs displayed the highest FRR value of above 96.5% after the entire fouling and cleaning experiment. The fabricated PVDF/N-Si-MWNTs hybrid membranes had excellent antibacterial efficacy, presenting maximum antibacterial efficacy of 98.0% and 95.6% against Staphylococcus aureus and Escherichia coli, respectively. Thus, the PVDF/N-Si-MWNTs membranes fabricated in this study are environment-friendly with both benign antibacterial and self-cleaning properties.