This study focused on the effects of membrane pore size and surface hydrophobicity on ultrafiltration (UF) membrane fouling caused by extracellular organic matter (EOM) from Microcystis aeruginosa. A hydrophilic membrane (cellulose acetate) with a molecular weight cutoff (MWCO) of 100kDa and hydrophobic membranes (polyethersulfone) with MWCO of 100, 30 and 10kDa were employed for UF experiments. The results indicated that the hydrophobic membrane suffered more adsorptive fouling, faster flux decline and worse fouling reversibility than the hydrophilic membrane when treating EOM solution. The membrane with larger pores exhibited worse flux reduction but less adsorptive fouling and superior flux recovery. Mass balances of dissolved organic carbon (DOC) content implied that more EOM passed through the hydrophilic membrane owing to a lack of hydrophobic adsorption and that the larger pore membrane allowed for higher EOM retention and a greater capacity for irreversibly deposited EOM. Fluorescence excitation-emission matrix (EEM) spectra coupling with regional integration were used to further analyze the fates of protein-like and humic-like substances during UF. Membrane pore size and surface hydrophobicity apparently influenced the transportation of protein-like substances, but they were of less importance for humic-like substances. In addition, four classic filtration models were introduced to analyze the fouling mechanisms. Cake formation was identified as the main mechanism for flux decline caused by EOM in this study, independent of membrane pore size and surface hydrophobicity. Display omitted •Effect of pore size and surface hydrophobicity on EOM fouling was investigated.•More hydrophobic and lower MWCO membranes suffer worse adsorptive fouling.•Stronger hydrophobicity leads to faster flux decline and worse reversibility.•Membrane with larger pores exhibits faster flux decline but better flux recovery.•Cake formation serves as the major mechanism of UF membrane fouling by EOM.