Iron is an important trace element in algal growth and water eutrophication. This study focused on the ultrafiltration (UF) membrane fouling mechanism by the intracellular organic matter (IOM) of Microcystis aeruginosa under different iron treatments. The results indicated that the membranes experienced faster flux decline and worse fouling reversibility when the IOM formed under low iron concentrations. In contrast, less IOM membrane fouling was found under normal and high iron concentrations. The mass balances of the dissolved organic carbon (DOC) content implied that the IOM in the low-iron treatment was associated with higher IOM retention and a higher capacity of reversibly deposited organics, whereas more IOM in the high-iron treatment passed through the UF membrane. The IOM in the low-iron treatment was composed of more biopolymer macromolecules, whereas the IOM in the high-iron treatment contained more UV-absorbing hydrophobic organics. The fluorescence excitation-emission matrix (EEM) spectra coupled with peak-fitting analysis implied that the fouling associated with protein-like components was more irreversible in the low-iron treatment than those in the normal- and high-iron treatments. Cake formation combined with intermediate blocking was identified as the main membrane fouling mechanism responsible for the flux decline caused by IOM solutions in the three iron treatments in this study.