Abstract: Membrane filtration technology has the advantages of well algae-water separation and sewage purification during the treatment of algae-rich water. Different pretreatment methods can affect the filtration characteristics and membrane fouling. In this study, three different pretreatment methods of diatomite, cotton plant and activated carbon were employed to filter Microcystis aeruginosa suspensions to compare their filtration characteristics, retention of algogenic organic matter and membrane fouling. The results revealed that the three pretreatment methods increased filtration flux and reduced membrane fouling. Among them, the diatomite pretreatment could increase the filtration flux by 915%, which was significantly better than other pretreatment. Activated carbon pretreatment could effectively adsorb aromatic protein-like compounds, and obviously decrease the resistance of irreversible chemical fouling. OCT and SEM analysis showed that no pretreatment caused the most serious membrane fouling, the lowest roughness and thickness of cake layer structure, while diatomite pretreatment could obviously mitigate membrane fouling by optimizing the cake layer structure. Meanwhile, the XDLVO theoretical results further confirmed that diatomite pretreatment had the best alleviating effect on membrane fouling. For further insight, the results provide valuable guidance for the development of membrane filtration of algae suspensions.