Extracellular organic matter (EOM) is considered an important cause of membrane fouling when harvesting Microcystis cells using filtration technology. Coagulation pre-treatment has increasingly been applied as an effective method to alleviate membrane fouling. However, the effects and mechanisms of EOM on coagulationmicrofiltration of Microcystis cells remain unclear. This study investigated the coagulation-microfiltration performance of EOM-free and EOM-containing Microcystis flos-aquae and explored the effect mechanisms of EOM from the perspective of floc characteristics and deposited algal cake structure. The results showed that the presence of EOM decreased the average flux from 4256.4 L/(m(2).h) to 3378.4 L/(m(2).h) at the optimal chitosan dosage of 15.11 mg/g. Electrostatic adsorption and/or bridging between carboxyl and amino/hydroxyl groups in EOM and chitosan resulted in a loose floc structure and high compressibility of the cake layer, thus reducing the filtration performance. In addition, interception of EOM in the cake layer contributed to membrane fouling during coagulation-microfiltration. These results revealed the mechanism by which EOM hinders coagulation filtration performance, which would be helpful for the development of efficient coagulation-filtration-based microalgal harvesting techniques.