Stable isotope fractionation of carbon and nitrogen in algal cells can be affected by photosynthesis, temperature, nutrient and CO2 concentrations, and cell size. As a consequence, carbon and nitrogen stable isotope techniques are not popular for determining algal growth rates. To counter these issues, this study used BG11 medium to cultivate Microcystis in the laboratory. First, the carbon and nitrogen stable isotope values of the culture medium and the algae are determined. Then, based on changes in isotope fractionation before and after cell division, a function μ = 1.32(1 + x)−0.52 relating growth rate and stable isotope fractionation is established. By substituting stable isotope values from Taihu Lake water and Microcystis into this function, the growth rate of the Microcystis in Taihu Lake is calculated to be 0.64 d−1 in May and 0.12 d−1 in September, with an average growth rate of 0.42 d−1. By incorporating most of the above-mentioned factors influencing isotope fractionation, this method can determine the growth rate of algae based directly on the stable isotope fractionation relationship, enabling simple and practical determination of algae growth rates.