The frequent outbreaks of cyanobacteria bloom are often accompanied by the generation and release of reduced phosphorus species (e.g., phosphine), which raises interesting questions regarding their potential algae-related effects. To clarify the physiological and biochemical responses of cyanobacteria to phosphine, Microcystis aeruginosa was treated with different concentrations of phosphine. Net photosynthetic rate, total antioxidant capacity (T-AOC), catalase (CAT) activity, and the concentrations of chlorophyll a, carotenoid and total protein were investigated and scanning electron microscopy (SEM) was conducted to elucidate the physiological and biochemical responses of M. aeruginosa to phosphine. The results showed that phosphine was beneficial to the growth of algal cells after M. aeruginosa acclimatized to the treatment of phosphine, and treatment with 2.48 × 10-2 mg/L phosphine had a greater positive effect on the growth and reproduction of M. aeruginosa than 7.51 × 10-3 mg/L phosphine, in which most algal cells were smooth and flat on day 16. Treatment with the high concentration of phosphine (7.51 × 10-2 mg/L) for 16 d reduced T-AOC, CAT activity, net photosynthetic rate, and the concentrations of chlorophyll a, carotenoid and total protein of M. aeruginosa to the minimums, resulting in the lysis and death of M. aeruginosa cells, which indicates phosphine has a toxic effect on the growth of algal cells. However, the high concentration of phosphine (7.51 × 10-2 mg/L) had a greater positive effect on the growth of M. aeruginosa cells than the lower two (7.51 × 10-3 mg/L and 2.48 × 10-2 mg/L) from 3 d to 12 d. Our findings provide insight into how phosphine potentially affects the growth of M. aeruginosa cells and the important roles of elevated phosphine on the outbreak of cyanobacteria bloom.