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The occurrence of cyanobacterial species, especially toxic ones, poses a great threat to coastal and estuary areas. In this study, the toxigenic <i>Microcystis aeruginosa</i> (<i>M</i>. <i>aeruginosa</i>) FACHB-905 was exposed to BG-11 medium with different salinities (1, 4, 7, 10 and 15 ppt) to investigate the physiological responses of this species in terms of oxidative stress, chl <i>a</i> fluorescence and microcystins (MCs) contamination. The results showed that low salinity (≤7 ppt) favored the electron transfer of photosystem II, which promoted the growth and photosynthesis of <i>M</i>. <i>aeruginosa</i> and induced MCs production. However, increased salinity (≥10 ppt) suppressed the growth and photosynthesis of <i>M</i>. <i>aeruginosa</i> and aggravated the oxidative stress of the strain. Salinity of 15 ppt reduced MCs contamination and caused irreversible damage to the photosynthetic system of <i>M</i>. <i>aeruginosa</i>, leading to the lysis and death of algal cells. These results indicated that changes in salinity exerted important regulations on the growth and MCs contamination of the toxic <i>M</i>. <i>aeruginosa</i>, which may provide a reference for the risk assessment of the harmful cyanobacterial species in the coastal and estuary areas.