Microcystis aeruginosa is a common cyanobacterium found in water blooms and often causes ecological harm. Antibiotics are also increasingly used for the prevention and treatment of bacterial infections in aquaculture. However, since most antibiotics cannot be fully metabolized, they enter the water environment and cause ecological impacts. In this paper, the effects of the two fluoroquinolone antibiotics (enrofloxacin and ciprofloxacin) on the population density and microcystins (MCs) production of M. aeruginosa were studied. It is of great significance for the ecological risk assessment of antibiotics in the water environment. The results showed that the 96h EC50 values of enrofloxacin and ciprofloxacin to M. aeruginosa were 56.10 mg/L and 49.80 mg/L, respectively, and the toxicity of ciprofloxacin to M. aeruginosa was slightly stronger than that of enrofloxacin. With the increase in the two antibiotic concentration, the growth inhibition rate (IR) increased, but when the concentration reached a certain level, the IR would reach its threshold. Long-term exposure to low concentrations of these two antibiotics is not only more likely to lead to the outbreak of M. aeruginosa, but also increase its toxin production capacity. The highest contents of MCs in enrofloxacin and ciprofloxacin groups were 95.539 μg/g and 93.720 μg/g, respectively. The MCs value of these three enrofloxacin treatment groups was more than above 51.8 times that of control group (CK) on the 4th day; from 8th day to 14th day, the MCs value of these three enrofloxacin treatment groups was more than above 3.2 times that of CK group. For ciprofloxacin, the MCs value of the treatment group was more than 64.98 times that of the CK group on the 4th day, and from 8th day to 14th day, the MCs value of the treatment group was more than 2.7 times that of the CK group. These findings provide crucial management rationale.