Cell-viability of cyanobacteria declines from development to decay stage during a successive bloom. Potassium permanganate (KMnO₄) has demonstrated to be a superior pre-oxidant to treat high-viability cyanobacteria compared to other common oxidants (e.g., chlorine), but whether it is feasible to treat low-viability cyanobacteria is unknown. Here, effects of KMnO₄ on membrane integrity, cyanotoxin fate and extracellular organic matters (EOMs) removal of high- and low-viability cyanobacteria were compared. Results showed that cell-viability of cyanobacteria could affect oxidant decay (k_decay), membrane damage (k_loss), and cyanotoxins release (k_i) and degradation (k_e) during KMnO₄ oxidation, similar to chlorination. However, unlike chlorination, initial low dosages of KMnO₄ (0.5 and 1 mg L^-1) minimized membrane damage for low-viability cyanobacteria (< 27%), and continuously decrease extracellular cyanotoxins, extracellular organic matters (EOMs), and aromatic compounds to some degrees (P<0.05). High dosages of KMnO₄ (> 2 mg L^-1) caused severe membrane destruction (> 89%) for low-viability cyanobacteria, leading to a fast increase of extracellular cyanotoxins within 1 h. However, total/extracellular cyanotoxins were oxidized to below the safety guideline of 1 μg L^-1 after being dosed with sufficient oxidant exposure. EOMs and aromatic compounds were also reduced by 5–18% (P<0.05). Additionally, KMnO₄-assisted coagulation significantly improved the removal of low-viability cyanobacteria (2–5 fold). Consequently, KMnO₄ could be a promising pre-oxidant to treat low-viability cyanobacteria at decay stage of a successive bloom.