Fortnightly investigations at 12 sampling sites in Meiliang Bay and Gonghu Bay of Lake Taihu (China) were carried out from June to early November 2010. The relationship between abiotic factors and cell density of different Microcystis species was analyzed using the interval maxima regression (IMR) to determine the optimum temperature and nutrient concentrations for growth of different Microcystis species. Our results showed that cell density of all the Microcystis species increased along with the increase of water temperature, but Microcystis aeruginosa adapted to a wide range of temperatures. The optimum total dissolved nitrogen concentrations for M. aeruginosa, Microcystis wesenbergii, Microcystis ichthyoblabe, and unidentified Microcystis were 3.7, 2.0, 2.4, and 1.9 mg L−1, respectively. The optimum total dissolved phosphorus concentrations for different species were M. wesenbergii (0.27 mg L−1) > M. aeruginosa (0.1 mg L−1) > M. ichthyoblabe (0.06 mg L−1) ≈ unidentified Microcystis, and the iron (Fe3+) concentrations were M. wesenbergii (0.73 mg L−1) > M. aeruginosa (0.42 mg L−1) > M. ichthyoblabe (0.35 mg L−1) > unidentified Microcystis (0.09 mg L−1). The above results suggest that if phosphorus concentration was reduced to 0.06 mg L−1 or/and iron concentration was reduced to 0.35 mg L−1 in Lake Taihu, the large colonial M. wesenbergii and M. aeruginosa would be replaced by small colonial M. ichthyoblabe and unidentified Microcystis. Thereafter, the intensity and frequency of the occurrence of Microcystis blooms would be reduced by changing Microcystis species composition.