A novel, highly hydrophilic nanocomposite additive, sulfonated carbon nano onion (SCNO), was synthesized from nanometer diamond by thermal annealing, phenylation and sulfonation. To examine the effects of the highly sulfonated spherical nanofillers, they were incorporated into polyethersulfone (PES) to fabricate nanocomposite ultrafiltration (UF) membranes through nonsolvent induced phase separation (NIPS) method. SCNO nanoparticles and PES/SCNO nanocomposite UF membranes were characterized using different characterization techniques including Fourier transform infrared spectroscopy, X-Ray diffraction, scanning electron microscope, atomic force microscopy and water contact angle. The performance of the PES/SCNO nanocomposite UF membranes was investigated with a cross-flow filtration system. The water contact angle gradually declined from 87.9° to 31° when the SCNO content varied from 0 to 1.5 wt%. The pure water flux of the PES/SCNO-1.0 membrane with SCNO content of 1.0% was up to 163.64 kg·m−2·h−1, which was 236% higher than the pristine PES membrane, along with the highest flux recovery ratio of 93.4% with bovine serum albumin. Overall, the incorporated SCNO nanoparticles opened a novel path to enhance the hydrophilicity, permeability and antifouling property of the PES-based UF membrane.