The photocatalytic modification technology presents a promising alternative for membrane fouling control. In this study, the polytetrafluoroethylene (PVDF) membrane was modified using atomic layer deposition (ALD) by coating three-dimensional (3D) TiO2/ZnO photocatalyst on membrane surface and pore walls. The TiO2/ZnO composite modified membrane was tailor-designed layer by layer at atomic scale with superior uniformity. The hydrophilicity, permeability, photocatalysis and anti-fouling performances of modified membranes were investigated in detail. Results showed that the modified membrane with cycle ratio of TiO2:ZnO=1:3 exhibited optimal versatilities under visible light irradiation. The photo-induced super-hydrophilicity was realized with a decline of 82.6% for the water contact angle and an increase of 33.5% for the pure water flux. Moreover, the 3D modified layer on membrane surface displayed excellent photocatalytic activity and stable reusability during methylene blue (MB) degradation. Fouling potential evaluation of humic acid (HA) revealed that the composite modified membrane (TiO2: ZnO=1:3) possessed excellent anti-fouling property due to the superior hydrophilicity and photocatalysis under visible light irradiation. Further exploration of the mechanism suggested the layer-by-layer proportionally formed hexagonal wurtzite ZnO and amorphous TiO2 created a novel type II heterostructure, which could effectively enhance the separation of photo-generated electron-holes. This novel photocatalytic membrane modified with layered TiO2/ZnO composite by ALD proved to have bright prospect for continuous wastewater treatment.