Due to the improper use, antibiotic residues became one of the highly persistent pollutants and have damaged the water ecosystem. In this paper, the growth characteristics, physiological condition and photosynthesis related genes of Microcystis aeruginosa were tested at five different mass concentrations of florfenicol. The results showed that in lower mass concentrations group (lower than 0.1 mg/L), the contents of chlorophyll a significantly increased, while no obvious effect on the phycobiliprotein content and the secretion of polysaccharide. In higher mass concentration group (higher than 1.0 mg/L), the synthesis of cyanobacteria chlorophyll a was inhibited, but the contents of phycobiliprotein and polysaccharides secreted increased. The photosynthesis related genes rbcL, psaB and psbD1 of Microcystis aeruginosa were changed with florfenicol treatment groups. The expression levels of rbcL and psaB genes were down-regulated in first three days, and up-regulated after 5th and 7th day exposure. The expression level of the psbD1 gene in the 0.1 mg/L group was not significantly different with the control group at 3-5 days after treatment, while the 1.0 mg/L group was significantly up-regulated than that of other groups. The results showed that 1.0 mg/L florfenicol in the water had a good impact on growth of Microcystis aeruginosa.