Morphology, the important feature of bloom-forming cyanobacteria, was studied for its impacts on the harmful cyanobacterial bloom (HCB) treatment by coagulative colloidal ozone microbubbles (CCOMBs). The globally-appeared HCB species – Microcystis aeruginosa (spherical cells, block mass colonies), Microcystis panniformis (spherical cells, flat penniform-like colonies) and Anabaena flos-aquae (filamentous morphology) were chosen as representative species. CCOMBs were generated by modifying the bubble surface and the gas core with coagulant and ozone, respectively. The removal of spherical cells and filaments was > 99.5% and ≤ 34.6%, individually, and the latter was ascribed to chain breakage. CCOMBs collected Microcystis panniformis via complexing with the fluorescent and non-fluorescent functional groups of cell colonies but captured Anabaena flos-aquae through the fluorescent ones. More Microcystis aeruginosa got membrane-damaged than Microcystis panniformis; nevertheless, the microcystin-LR (MC-LR) removal was guaranteed through efficiently oxidizing the released MC-LR. Although the outer peptidoglycan sheet of Anabaena flos-aquae was destroyed, the inner cyte membrane remained intact, preventing intracellular MC-LR from releasing. The HCBs dominated by single species with spherical cells were more readily treated than those with co-occurred species. The toxicological tests imply that, as a robust tool for HCB treatment, the CCOMB technology could be eco-environmentally friendly to the aquatic environment.