OBJECTIVE: To study the inhibition effect on blue-green algae of higher aquatic plants with their rhizosphere microorganisms and its mathematical model. METHODS: The inhibitory effects of sterile and containing bacterium Myriophyllum verticillatum L root extracts on Microcystis aeruginosa were studied respectively, and the difference-differential equation of algal growth and partial functional differential equation were established according to the algal inhibiting effect. RESULTS: (1) The sterile and containing bacterium Myriophyllum verticillatum L root extracts showed at some degree inhibitory effects on M. aeruginosa, and containing bacteria root extract had more potent algal inhibiting effect, and very lower half maximal effective concentration (EC50). (2) The established inhibitory mathematical models can effectively predicted and calculated algal densities and EC50 at varying exposure time and different environment. CONCLUSION: The rhizospheric microorganisms can effectively enhanced the inhibiting effect of Myriophyllum verticillatum L on M. aeruginosa.