The effects of different concentrations (100,150,200,250 mg/L) and different particle sizes (0–75µm, 75–120µm, 120–150µm, 150–500µm) on soluble protein content, SOD and CAT activity, MDA content, chlorophyll a content and photosynthetic parameters of Microcystis flos-aquae were studied, the mechanism of the effect of suspended particulate matter on the physiology and biochemistry of Microcystis flos-aquae was discussed. The results showed that the soluble protein content of Microcystis flos-aquae did not change obviously after being stressed by suspended particles of different concentration/diameter. The SOD activity of Microcystis flos-aquae increased at first and then decreased with the increase of the concentration of suspended particulate matter. The SOD activity of Microcystis flos-aquae reached 28.03 U/mL when the concentration of suspended particulate matter was 100 mg/L. The CAT activity of Microcystis flos-aquae increased with the increase of the concentration of suspended particles, and reached the maximum value of 12.45 U/mgprot in the concentration group of 250 mg/L, showing a certain dose-effect. The effect of small particle size on SOD, CAT and MDA of Microcystis flos-aquae was more significant than that of large particle size. The larger the concentration and the smaller the particle size, the stronger the attenuation of light and the lower the content of chlorophyll a. Both Fv/Fm and Fv/F0 of Microcystis flos-aquae increased at first and then decreased under different concentration/size of suspended particles. The relative electron transfer rate gradually returned to the normal level with the passage of time. There was no significant difference in α value between treatment group and control group, ETRmax and Ik decreased.