The covalently functionalized cellulose nanocrystal (CNC) composites were synthesized by bonding common bactericides, such as dodecyl dimethyl benzyl ammonium chloride (DDBAC), ZnO and graphene oxide (GO) nanosheets, onto the CNC's surface. Then, the DDBAC/CNC, ZnO/CNC and GO/CNC nanocomposites modified polyvinylidene fluoride (PVDF) ultrafiltration membranes were fabricated by a simple one-step non-solvent induced phase separation (NIPS) process. The resultant hybrid membranes possessed porous and rough surfaces with more finger-like macropores that even extended through the entire cross-section. The hydrophilicity, permeability, antibacterial and antifouling performance and mechanism of the hybrid ultrafiltration membranes were evaluated and compared in detail, aiming at screening a superior hybrid membrane for practical application in micro-polluted source water purification. Among these newly-developed hybrid membranes, GO/CNC/PVDF exhibited an enhanced perm-selectivity with a water flux of 230 L/(m2 h bar) and humic acid rejection of 92%, the improved antibacterial activity (bacteriostasis rate of 93%) and antifouling performance (flux recovery rate (FRR) of >90%) being due to the optimized pore structure, higher surface roughness, incremental hydrophilicity and electronegativity. A lower biofouling level after three weeks' filtration of the actual micro-polluted source water further demonstrated that embedding the hydrophilic and antibacterial GO/CNC nanocomposite into the polymer matrix is an effective strategy to improve membrane anti-biofouling ability.