Membrane filtration is a promising approach for harvesting microalgae for production of biofuel and high-value products. Membrane fouling is the most limiting factor for filtration operation as it causes low flow flux, high transmembrane pressure and high maintenance cost associated with membrane backwash and replacement. In the present study, the harvesting efficiency and the membrane fouling properties of a bench-scale ultrafiltration system with a submerged flat-sheet ceramic membrane were investigated for harvesting green microalgae, Chlorella vulgaris, under sub- and super-critical flux. The fouling mechanism (cake layer, gel layer and membrane pore blocking) was systematically analyzed to illustrate the possible fouling profiles at sub and super-critical flux. The results showed that the productivity for harvesting microalgal cells under super-critical flux condition was three times higher than sub-critical flux condition, with the fouling rates 8 times higher as well. The increase in irreversible membrane fouling was attributed as the main cause of the membrane resistance increase at the super-critical flux condition although the resistance of cake layer was the highest for both conditions. SMPs, aromatic protein and humic-like organics of microalgae broth contribute to the irreversible membrane fouling.