The outbreak of cyanobacterial blooms in water can cause serious harm to water supply safety and human health, which has become one of the major water environmental problems in the present world. In this paper, the representative Microcystis aeruginosa blooms were studied by the eutrophic microcosmic simulation device between natural lake system and test in laboratory scale. Toxic Microcystis aeruginosa FACHB-905 and non-toxic Microcystis aeruginosa FACHB-469 were used to simulate algal blooms in different nutrient conditions. The study of stratified EPS extracted from different vegetative and growth stages of Microcystis aeruginosa showed that high nutritional conditions can induce Microcystis aeruginosa to produce more extracellular polysaccharides, while low nutrient conditions can affect the fluorescence components in the SL-EPS (Soluble EPS) of Microcystis aeruginosa. Furthermore, the proteins in TB-EPS (Tightly bound EPS) will gradually release to SL-EPS and LB-EPS (loosely bound EPS) during the bloom, which can decrease from 34% in the initial growth period to 20%. The tryptophan-like substances in SL-EPS and TB-EPS, and the humic-acid-like substances in SL-EPS have a significant impact on the Microcystis aeruginosa blooms. Finally, all these results are expected to be of use in the study of the algal blooming outbreak early warning and control problems.