Occurrence of toxic cyanobacterial blooms in natural freshwaters could impair drinking water quality. Chlorine was often employed as an oxidant to treat algal-laden source waters in drinking water treatment plants. However, previous studies only focused on high-viability cyanobacteria at exponential phase. Whether the change of cell-viability of cyanobacteria could affect chlorination was unknown. Here, high- and low-viability Microcystis were collected from a whole life cycle of cyanobacteria in lab-scale, and effects of chlorination on membrane integrity and toxin fate of high- and low-viability Microcystis were subsequently investigated. Results showed chlorine exposure was lower for low-viability cells than high-viability cells with the same initial chlorine dosage, but low-viability cells were less resistant to chlorination, leading to higher rate of membrane damage (k_loss) and intracellular toxin release (k_i). For high-viability cells, there was no increase of extracellular toxin with sufficient chlorine exposure whereas it showed a continuous increase for low-viability cells mainly due to its lower rate of extracellular toxin degradation (k_e, 26 ± 8 M^-1 s^-1) than intracellular toxin release (k_i, 110 ± 16 M^-1 s^-1) (k_e < k_i). Besides, total toxin could be completely oxidized for high-viability cells with sufficient chlorine exposure (>30 mg min L^-1) whereas chlorination could not work well for low-viability cells even with chlorine exposure of as high as 36 mg min L^-1. These findings indicated chlorination may not be a feasible option to treat low-viability cyanobacteria during decline stage of cyanobacterial blooms.