The effects of different concentrations (100, 150, 200, 250mg/L) and different particle sizes (0-75μm, 75-120μm, 120-150μm, 150-500μm) on the soluble protein content, superoxide dismutase (SOD) and catalase (CAT) activity, malondialdehyde (MDA) content, chlorophyll a (Chla) content, and photosynthetic parameters of Microcystis flos-aquae were studied, and 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 noticeably after being stressed by suspended particles of different concentrations/diameters. The SOD activity of Microcystis flos-aquae first increased and then decreased with increasing suspended particulate matter concentrations. The SOD activity of Microcystis flos-aquae reached 28.03 U/mL when the concentration of suspended particulate matter was 100mg/L. The CAT activity of Microcystis flos-aquae increased with increasing concentrations of suspended particles and reached a maximum value of 12.45 U/mg prot in the 250mg/L concentration group, showing a certain dose effect. Small particles had a more significant effect on SOD, CAT, and MDA in Microcystis flos-aquae than large particles. The larger the concentration was and the smaller the particle size was, the stronger the attenuation of light and the lower the content of Chla. Both the maximum quantum yield of PSII (Fv/Fm) and the potential photosynthetic activity of PSII (Fv/F0) of Microcystis flos-aquae increased at first and then decreased under different concentrations/sizes of suspended particles. The relative electron transfer rate gradually returned to a normal level over time. There was no significant difference in the initial slope (α) value between the treatment group and the control group, and the maximum photo synthetic rate (ETRmax) and the semilight saturation (Ik) decreased.