The objective of this study was to determine the influence of Tanfloc on Microcystis aeruginosa cell integrity, microcystin-LR (MC-LR), and proteins during flocculation and floc storage. The effects of Tanfloc addition, stirring, and floc storage time were considered to minimize cell damage and the release of MC-LR and proteins. Optimal flocculation conditions (Tanfloc dosage 10.42 mg L−1, rapid agitation for 0.36 min at 568.88 rpm and slow agitation for 14.14 min at 12.1 rpm) were obtained using the response surface methodology. Up to 98.9% of the M. aeruginosa cells were removed intact at low Tanfloc dosage. During floc storage, Tanfloc initially protected the cells. After 8 d, large-scale cell lysis occurred because Tanfloc had substantially decomposed. Nevertheless, Tanfloc also extended the extracellular MC-LR and protein release time to 8 d. This delay ensured adequate time to decontaminate sludge containing the algae, thereby reducing the risk of secondary pollution. In addition, the low cost of Tanfloc facilitates its widespread application in the management of harmful algal blooms.