Flocculation-filtration treatment with cationic polymers and a rotary drum filter is an effective method to control Microcystis bloom by separating Microcystis from water. However, flocculation and corresponding removal are significantly affected by dissolved organic matters, of which extracellular organic matter (EOM) of Microcystis is the main source during Microcystis blooms. Hence, this study investigated the effect of EOM on the removal of Microcystis by using flocculation with cationic polyacrylamide (CPAM) and filtration with 100-mu m filter. Results showed that the removal efficiency increased with the growth of Microcystis and was attributed to the accumulated EOM. With EOM > 2.5 mg/L extracted from stationary growth period, the cells could form large flocs with CPAM, over 90 % of which could be detained by a 100-mu m sieve. Scanning electron microscope images showed that EOM interacted with CPAM and formed complexes, which bridged between the cells more strongly. Meanwhile, the removal was affected by EOM characteristics and had a positive correlation with the proportion of protein and polysaccharide in the EOM, which were usually regarded as polymers. The high-molecular weight (MW > 30 kDa) fraction was thus identified as an effective component in EOM to facilitate the formation of large and compact flocs, especially the fraction with MW > 100 kDa. This study partly revealed the differences in the removal efficiency of Microcystis from the perspective of the concentration and characteristic of EOM, and aid the understanding of the interaction between CPAM and high-MW EOM fraction for the formation of large and compact flocs.