Allelopathic interactions amongst phytoplankton are considered an important factor contributing to species competition and succession in aquatic ecosystems, but their mechanisms in plankton dynamics are poorly described. In this study, whether toxic Microcystis aeruginosa could affect the growth of Chlorella vulgaris and Kirchneriella sp. was examined according to filtrate experiments at different cultivation phases. Results indicated that M. aeruginosa filtrate significantly influenced the growth and morphological characteristics of the two target green algae, which were dependent on the cultivation growth phase of filtrate and target strain. At the beginning of the experiment, the formation of a large C. vulgaris colony was induced by M. aeruginosa filtrate. The effects of filtrate in the stationary phase (SP) was more significant than that of the exponential phase (EP). Subsequently, the colonies gradually broke into small colonies or single cells. The growth rate of C. vulgaris was finally promoted in the filtrate treatment. For Kirchneriella sp., the colonies formed and remained in M. aeruginosa filtrate under EP until the end of the experiment. Smaller colonies were observed in Kirchneriella sp. by M. aeruginosa filtrate under SP than those in the control, and larger colonies were not detected. The growth rate of Kirchneriella sp. was inhibited in the filtrate of EP but was promoted in SP. This study provided new insights into the interaction between the morphological responses and growth effects of algae and proposed a new theoretical basis for algal succession in aquatic ecosystems.