Microcystis aeruginosa is the main species during alga bloom in inland eutrophic lakes. We consider that Microcystis aeruginosa consists of cytoplasm and chloroplast for simulating optical characteristics based on the two-layered spherical geometry. The central real refractive index value and volume ratio of chloroplast are calculated through the method of loop iterations. Meanwhile, based on the Kramers-Kronig relationship, the refractive index value of cytoplasm and chloroplast could be obtained. Finally, the absorption and scattering properties of Microcystis aeruginosa are simulated using the Aden-Kerker theory and particle size distribution. The results show that the relative errors between modeled and measured scattering and absorption efficiency factors are 3.4% and 4.3%, respectively. In comparison with the simulation based on Mie theory, the two-layered spherical model shows a better simulation accuracy of the backscattering properties.