This study aimed to investigate the performance of chitosan-modified nano-sized montmorillonite (CTS/NMMT) during the flocculation of Microcystis aeruginosa (MA). The release of intracellular microcystins (MCs) caused by the damage of intact MA cells during the flocculation and floc storage processes was also comprehensively evaluated through scanning electron microscopy (SEM) and measurement of K(+) and Mg(2+) release. With the application of the Box-Behnken experimental design combined with response surface methodology, the quadratic statistical model was established to predict and optimize the interactive effects of content of CTS/NMMT, weight ratio of NMMT to CTS, and agitation time on the removal efficiency of MA cells. A maximum removal of 94.7 % MA cells was observed with content of CTS/NMMT 300-320 mg L(-1), weight ratio of NMMT to CTS 14-16, and agitation time 16-50 min. During the flocculation process, CTS/NMMT aggregated MA cells as flocs and served as a protection shield for cells. The extracellular and intracellular microcystin-leucine-arginine (MC-LR) decreased remarkably and the yield of intracellular MC-LR showed a decreasing trend during the flocculation. The cell integrity was slightly damaged by the mechanical actions rather than by the flocculant. During the floc storage process, cell lysis and membrane damage were remarkably aggravated. The noticeable increase of K(+) and Mg(2+) release indicated that CTS/NMMT damaged the integrity of most MA cells in the flocs and liberated the intracellular MC-LR. Meanwhile, NMMT and CTS polymers assisted the adsorptive removal of extracellular MC-LR released to water. The flocs should be timely treated within 12 h to prevent the leakage of MCs.